CA2469738A1 - Expression vectors encoding epitopes of target-associated antigens and methods for their design - Google Patents
Expression vectors encoding epitopes of target-associated antigens and methods for their design Download PDFInfo
- Publication number
- CA2469738A1 CA2469738A1 CA 2469738 CA2469738A CA2469738A1 CA 2469738 A1 CA2469738 A1 CA 2469738A1 CA 2469738 CA2469738 CA 2469738 CA 2469738 A CA2469738 A CA 2469738A CA 2469738 A1 CA2469738 A1 CA 2469738A1
- Authority
- CA
- Canada
- Prior art keywords
- hla
- epitope
- seq
- housekeeping
- epitopes
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Abandoned
Links
- 108091007433 antigens Proteins 0.000 title claims abstract description 52
- 102000036639 antigens Human genes 0.000 title claims abstract description 52
- 239000000427 antigen Substances 0.000 title claims abstract description 51
- 238000000034 method Methods 0.000 title claims abstract description 47
- 238000013461 design Methods 0.000 title description 4
- 239000013604 expression vector Substances 0.000 title description 4
- 108090000765 processed proteins & peptides Proteins 0.000 claims abstract description 141
- 102000004196 processed proteins & peptides Human genes 0.000 claims abstract description 98
- 229920001184 polypeptide Polymers 0.000 claims abstract description 68
- 239000000758 substrate Substances 0.000 claims abstract description 67
- 102000004245 Proteasome Endopeptidase Complex Human genes 0.000 claims abstract description 53
- 108090000708 Proteasome Endopeptidase Complex Proteins 0.000 claims abstract description 53
- 239000013598 vector Substances 0.000 claims abstract description 50
- 238000012545 processing Methods 0.000 claims abstract description 37
- 210000001744 T-lymphocyte Anatomy 0.000 claims abstract description 30
- 238000013519 translation Methods 0.000 claims abstract description 19
- 239000000203 mixture Substances 0.000 claims abstract description 18
- 230000003213 activating effect Effects 0.000 claims abstract description 4
- 210000004027 cell Anatomy 0.000 claims description 99
- 206010028980 Neoplasm Diseases 0.000 claims description 16
- 230000003053 immunization Effects 0.000 claims description 14
- 238000003556 assay Methods 0.000 claims description 12
- 238000002649 immunization Methods 0.000 claims description 12
- 238000000338 in vitro Methods 0.000 claims description 12
- 108091033319 polynucleotide Proteins 0.000 claims description 12
- 102000040430 polynucleotide Human genes 0.000 claims description 12
- 239000002157 polynucleotide Substances 0.000 claims description 12
- 108020001507 fusion proteins Proteins 0.000 claims description 8
- 102000037865 fusion proteins Human genes 0.000 claims description 8
- 101100462972 Mus musculus Pcdh8 gene Proteins 0.000 claims description 6
- 238000012163 sequencing technique Methods 0.000 claims description 6
- 238000004949 mass spectrometry Methods 0.000 claims description 5
- 244000000056 intracellular parasite Species 0.000 claims description 4
- 238000004128 high performance liquid chromatography Methods 0.000 claims description 3
- 230000001131 transforming effect Effects 0.000 claims description 2
- 108010088729 HLA-A*02:01 antigen Proteins 0.000 description 94
- 108010058607 HLA-B Antigens Proteins 0.000 description 86
- 102000006390 HLA-B Antigens Human genes 0.000 description 86
- 210000001151 cytotoxic T lymphocyte Anatomy 0.000 description 59
- 102000011786 HLA-A Antigens Human genes 0.000 description 50
- 108010075704 HLA-A Antigens Proteins 0.000 description 50
- 108090000623 proteins and genes Proteins 0.000 description 42
- 206010022000 influenza Diseases 0.000 description 40
- 241000713772 Human immunodeficiency virus 1 Species 0.000 description 38
- 235000018102 proteins Nutrition 0.000 description 29
- 102000004169 proteins and genes Human genes 0.000 description 29
- 108700018351 Major Histocompatibility Complex Proteins 0.000 description 25
- 238000003776 cleavage reaction Methods 0.000 description 25
- 230000007017 scission Effects 0.000 description 25
- 230000020382 suppression by virus of host antigen processing and presentation of peptide antigen via MHC class I Effects 0.000 description 24
- 235000001014 amino acid Nutrition 0.000 description 22
- 238000003491 array Methods 0.000 description 21
- 150000001413 amino acids Chemical class 0.000 description 20
- 102100028971 HLA class I histocompatibility antigen, C alpha chain Human genes 0.000 description 19
- 241000725303 Human immunodeficiency virus Species 0.000 description 18
- 108010010995 MART-1 Antigen Proteins 0.000 description 18
- 102100028389 Melanoma antigen recognized by T-cells 1 Human genes 0.000 description 18
- 241000700605 Viruses Species 0.000 description 18
- 230000004044 response Effects 0.000 description 18
- 108700020134 Human immunodeficiency virus 1 nef Proteins 0.000 description 17
- 230000006870 function Effects 0.000 description 17
- 150000007523 nucleic acids Chemical class 0.000 description 17
- 241000282414 Homo sapiens Species 0.000 description 16
- 239000013612 plasmid Substances 0.000 description 16
- 108010074032 HLA-A2 Antigen Proteins 0.000 description 15
- 102000025850 HLA-A2 Antigen Human genes 0.000 description 15
- 230000000694 effects Effects 0.000 description 15
- 101000986084 Homo sapiens HLA class I histocompatibility antigen, C alpha chain Proteins 0.000 description 14
- 108020004999 messenger RNA Proteins 0.000 description 14
- 102000039446 nucleic acids Human genes 0.000 description 14
- 108020004707 nucleic acids Proteins 0.000 description 14
- 101710122228 Epstein-Barr nuclear antigen 2 Proteins 0.000 description 13
- 125000003275 alpha amino acid group Chemical group 0.000 description 13
- 241000701806 Human papillomavirus Species 0.000 description 11
- 230000002093 peripheral effect Effects 0.000 description 11
- 102100025570 Cancer/testis antigen 1 Human genes 0.000 description 10
- 108020004414 DNA Proteins 0.000 description 10
- 101000856237 Homo sapiens Cancer/testis antigen 1 Proteins 0.000 description 10
- 102000003425 Tyrosinase Human genes 0.000 description 10
- 108060008724 Tyrosinase Proteins 0.000 description 10
- 239000012634 fragment Substances 0.000 description 10
- 238000012360 testing method Methods 0.000 description 10
- 229960005486 vaccine Drugs 0.000 description 10
- 244000205754 Colocasia esculenta Species 0.000 description 9
- 235000006481 Colocasia esculenta Nutrition 0.000 description 9
- 108010054198 HLA-B*27:05 antigen Proteins 0.000 description 9
- 108010091938 HLA-B7 Antigen Proteins 0.000 description 9
- 102000008949 Histocompatibility Antigens Class I Human genes 0.000 description 9
- 108010088652 Histocompatibility Antigens Class I Proteins 0.000 description 9
- 102000014150 Interferons Human genes 0.000 description 9
- 108010050904 Interferons Proteins 0.000 description 9
- 210000005170 neoplastic cell Anatomy 0.000 description 9
- 238000012216 screening Methods 0.000 description 9
- 102220378376 HLA-B*2705 Human genes 0.000 description 8
- 241000829100 Macaca mulatta polyomavirus 1 Species 0.000 description 8
- -1 for example Substances 0.000 description 8
- 230000028993 immune response Effects 0.000 description 8
- 238000001727 in vivo Methods 0.000 description 8
- 108010039075 HLA-B8 Antigen Proteins 0.000 description 7
- 108091034117 Oligonucleotide Proteins 0.000 description 7
- JLCPHMBAVCMARE-UHFFFAOYSA-N [3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methyl [5-(6-aminopurin-9-yl)-2-(hydroxymethyl)oxolan-3-yl] hydrogen phosphate Polymers Cc1cn(C2CC(OP(O)(=O)OCC3OC(CC3OP(O)(=O)OCC3OC(CC3O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c3nc(N)[nH]c4=O)C(COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3CO)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cc(C)c(=O)[nH]c3=O)n3cc(C)c(=O)[nH]c3=O)n3ccc(N)nc3=O)n3cc(C)c(=O)[nH]c3=O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)O2)c(=O)[nH]c1=O JLCPHMBAVCMARE-UHFFFAOYSA-N 0.000 description 7
- 125000000539 amino acid group Chemical group 0.000 description 7
- 238000001802 infusion Methods 0.000 description 7
- 229940079322 interferon Drugs 0.000 description 7
- 108010031111 EBV-encoded nuclear antigen 1 Proteins 0.000 description 6
- 108010014597 HLA-B44 Antigen Proteins 0.000 description 6
- 108700039791 Hepatitis C virus nucleocapsid Proteins 0.000 description 6
- 210000000612 antigen-presenting cell Anatomy 0.000 description 6
- 239000002299 complementary DNA Substances 0.000 description 6
- 230000029087 digestion Effects 0.000 description 6
- 230000002163 immunogen Effects 0.000 description 6
- 201000001441 melanoma Diseases 0.000 description 6
- 238000012546 transfer Methods 0.000 description 6
- 101710122231 Epstein-Barr nuclear antigen 3 Proteins 0.000 description 5
- 108010052199 HLA-C Antigens Proteins 0.000 description 5
- 101000892862 Homo sapiens Glutamate carboxypeptidase 2 Proteins 0.000 description 5
- 241000700588 Human alphaherpesvirus 1 Species 0.000 description 5
- FFEARJCKVFRZRR-BYPYZUCNSA-N L-methionine Chemical compound CSCC[C@H](N)C(O)=O FFEARJCKVFRZRR-BYPYZUCNSA-N 0.000 description 5
- 101000702488 Rattus norvegicus High affinity cationic amino acid transporter 1 Proteins 0.000 description 5
- 238000004458 analytical method Methods 0.000 description 5
- 201000011510 cancer Diseases 0.000 description 5
- 230000001413 cellular effect Effects 0.000 description 5
- 230000009089 cytolysis Effects 0.000 description 5
- 210000004443 dendritic cell Anatomy 0.000 description 5
- 230000001939 inductive effect Effects 0.000 description 5
- 239000012678 infectious agent Substances 0.000 description 5
- 229930182817 methionine Natural products 0.000 description 5
- 238000002560 therapeutic procedure Methods 0.000 description 5
- 210000001519 tissue Anatomy 0.000 description 5
- 108091026890 Coding region Proteins 0.000 description 4
- 102100041003 Glutamate carboxypeptidase 2 Human genes 0.000 description 4
- VDCRBJACQKOSMS-JSGCOSHPSA-N Gly-Phe-Val Chemical compound [H]NCC(=O)N[C@@H](CC1=CC=CC=C1)C(=O)N[C@@H](C(C)C)C(O)=O VDCRBJACQKOSMS-JSGCOSHPSA-N 0.000 description 4
- 108010075326 HLA-B51 Antigen Proteins 0.000 description 4
- 108010084873 Human Immunodeficiency Virus nef Gene Products Proteins 0.000 description 4
- 241000701024 Human betaherpesvirus 5 Species 0.000 description 4
- 241001529936 Murinae Species 0.000 description 4
- 241000699666 Mus <mouse, genus> Species 0.000 description 4
- 241000699670 Mus sp. Species 0.000 description 4
- 108091008874 T cell receptors Proteins 0.000 description 4
- 101710192266 Tegument protein VP22 Proteins 0.000 description 4
- 230000002902 bimodal effect Effects 0.000 description 4
- 210000000987 immune system Anatomy 0.000 description 4
- 208000015181 infectious disease Diseases 0.000 description 4
- 208000037797 influenza A Diseases 0.000 description 4
- 108010061181 influenza matrix peptide (58-66) Proteins 0.000 description 4
- 239000003999 initiator Substances 0.000 description 4
- NOESYZHRGYRDHS-UHFFFAOYSA-N insulin Chemical compound N1C(=O)C(NC(=O)C(CCC(N)=O)NC(=O)C(CCC(O)=O)NC(=O)C(C(C)C)NC(=O)C(NC(=O)CN)C(C)CC)CSSCC(C(NC(CO)C(=O)NC(CC(C)C)C(=O)NC(CC=2C=CC(O)=CC=2)C(=O)NC(CCC(N)=O)C(=O)NC(CC(C)C)C(=O)NC(CCC(O)=O)C(=O)NC(CC(N)=O)C(=O)NC(CC=2C=CC(O)=CC=2)C(=O)NC(CSSCC(NC(=O)C(C(C)C)NC(=O)C(CC(C)C)NC(=O)C(CC=2C=CC(O)=CC=2)NC(=O)C(CC(C)C)NC(=O)C(C)NC(=O)C(CCC(O)=O)NC(=O)C(C(C)C)NC(=O)C(CC(C)C)NC(=O)C(CC=2NC=NC=2)NC(=O)C(CO)NC(=O)CNC2=O)C(=O)NCC(=O)NC(CCC(O)=O)C(=O)NC(CCCNC(N)=N)C(=O)NCC(=O)NC(CC=3C=CC=CC=3)C(=O)NC(CC=3C=CC=CC=3)C(=O)NC(CC=3C=CC(O)=CC=3)C(=O)NC(C(C)O)C(=O)N3C(CCC3)C(=O)NC(CCCCN)C(=O)NC(C)C(O)=O)C(=O)NC(CC(N)=O)C(O)=O)=O)NC(=O)C(C(C)CC)NC(=O)C(CO)NC(=O)C(C(C)O)NC(=O)C1CSSCC2NC(=O)C(CC(C)C)NC(=O)C(NC(=O)C(CCC(N)=O)NC(=O)C(CC(N)=O)NC(=O)C(NC(=O)C(N)CC=1C=CC=CC=1)C(C)C)CC1=CN=CN1 NOESYZHRGYRDHS-UHFFFAOYSA-N 0.000 description 4
- 239000003446 ligand Substances 0.000 description 4
- 210000001165 lymph node Anatomy 0.000 description 4
- 238000011330 nucleic acid test Methods 0.000 description 4
- 238000011830 transgenic mouse model Methods 0.000 description 4
- POVNCJSPYFCWJR-USZUGGBUSA-N (4s)-4-[[(2s)-2-[[(2s)-2-amino-3-(4-hydroxyphenyl)propanoyl]amino]-4-methylpentanoyl]amino]-5-[(2s)-2-[[2-[(2s)-2-[[(2s)-1-[[(2s,3r)-1-[[(1s)-1-carboxy-2-methylpropyl]amino]-3-hydroxy-1-oxobutan-2-yl]amino]-3-methyl-1-oxobutan-2-yl]carbamoyl]pyrrolidin-1- Chemical compound C([C@H](N)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CCC(O)=O)C(=O)N1[C@@H](CCC1)C(=O)NCC(=O)N1[C@@H](CCC1)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H]([C@@H](C)O)C(=O)N[C@@H](C(C)C)C(O)=O)C1=CC=C(O)C=C1 POVNCJSPYFCWJR-USZUGGBUSA-N 0.000 description 3
- 241000894006 Bacteria Species 0.000 description 3
- 101710122233 Epstein-Barr nuclear antigen 4 Proteins 0.000 description 3
- 101710122229 Epstein-Barr nuclear antigen 6 Proteins 0.000 description 3
- 241000588724 Escherichia coli Species 0.000 description 3
- 101100279830 Friend murine leukemia virus env gene Proteins 0.000 description 3
- 102220372951 HLA-A*3101 Human genes 0.000 description 3
- 108010013476 HLA-A24 Antigen Proteins 0.000 description 3
- 108010086377 HLA-A3 Antigen Proteins 0.000 description 3
- 108010017588 HLA-B*52:01 antigen Proteins 0.000 description 3
- 108010004141 HLA-B35 Antigen Proteins 0.000 description 3
- 108010037618 HLA-C*08 antigen Proteins 0.000 description 3
- 101000606090 Homo sapiens Tyrosinase Proteins 0.000 description 3
- 102100022430 Melanocyte protein PMEL Human genes 0.000 description 3
- 102000000440 Melanoma-associated antigen Human genes 0.000 description 3
- 108050008953 Melanoma-associated antigen Proteins 0.000 description 3
- 241000713333 Mouse mammary tumor virus Species 0.000 description 3
- 102000035195 Peptidases Human genes 0.000 description 3
- 108091005804 Peptidases Proteins 0.000 description 3
- KLYYKKGCPOGDPE-OEAJRASXSA-N Phe-Thr-Leu Chemical compound [H]N[C@@H](CC1=CC=CC=C1)C(=O)N[C@@H]([C@@H](C)O)C(=O)N[C@@H](CC(C)C)C(O)=O KLYYKKGCPOGDPE-OEAJRASXSA-N 0.000 description 3
- 239000004365 Protease Substances 0.000 description 3
- 102100030086 Receptor tyrosine-protein kinase erbB-2 Human genes 0.000 description 3
- 241000700584 Simplexvirus Species 0.000 description 3
- 102000016266 T-Cell Antigen Receptors Human genes 0.000 description 3
- 210000003719 b-lymphocyte Anatomy 0.000 description 3
- 230000001580 bacterial effect Effects 0.000 description 3
- 239000003795 chemical substances by application Substances 0.000 description 3
- 230000001684 chronic effect Effects 0.000 description 3
- 230000000295 complement effect Effects 0.000 description 3
- 230000001461 cytolytic effect Effects 0.000 description 3
- 230000001086 cytosolic effect Effects 0.000 description 3
- 229940079593 drug Drugs 0.000 description 3
- 239000003814 drug Substances 0.000 description 3
- 238000009472 formulation Methods 0.000 description 3
- 108010007811 human immunodeficiency virus p17 gag peptide Proteins 0.000 description 3
- 230000003308 immunostimulating effect Effects 0.000 description 3
- 238000004519 manufacturing process Methods 0.000 description 3
- 239000011159 matrix material Substances 0.000 description 3
- 238000012737 microarray-based gene expression Methods 0.000 description 3
- 230000003278 mimic effect Effects 0.000 description 3
- 238000012243 multiplex automated genomic engineering Methods 0.000 description 3
- 239000002773 nucleotide Substances 0.000 description 3
- 125000003729 nucleotide group Chemical group 0.000 description 3
- 229920001481 poly(stearyl methacrylate) Polymers 0.000 description 3
- 230000008488 polyadenylation Effects 0.000 description 3
- 230000001737 promoting effect Effects 0.000 description 3
- 230000010076 replication Effects 0.000 description 3
- 230000004936 stimulating effect Effects 0.000 description 3
- 230000001225 therapeutic effect Effects 0.000 description 3
- 238000013518 transcription Methods 0.000 description 3
- 230000035897 transcription Effects 0.000 description 3
- 238000009966 trimming Methods 0.000 description 3
- 241000701161 unidentified adenovirus Species 0.000 description 3
- 238000002255 vaccination Methods 0.000 description 3
- 230000003612 virological effect Effects 0.000 description 3
- LKKMLIBUAXYLOY-UHFFFAOYSA-N 3-Amino-1-methyl-5H-pyrido[4,3-b]indole Chemical compound N1C2=CC=CC=C2C2=C1C=C(N)N=C2C LKKMLIBUAXYLOY-UHFFFAOYSA-N 0.000 description 2
- 102100037982 Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A Human genes 0.000 description 2
- 241000283690 Bos taurus Species 0.000 description 2
- 201000009030 Carcinoma Diseases 0.000 description 2
- 241000701022 Cytomegalovirus Species 0.000 description 2
- 108010069621 Epstein-Barr virus EBV-associated membrane antigen Proteins 0.000 description 2
- LFQSCWFLJHTTHZ-UHFFFAOYSA-N Ethanol Chemical compound CCO LFQSCWFLJHTTHZ-UHFFFAOYSA-N 0.000 description 2
- 241000287828 Gallus gallus Species 0.000 description 2
- AAHSHTLISQUZJL-QSFUFRPTSA-N Gly-Ile-Ile Chemical compound [H]NCC(=O)N[C@@H]([C@@H](C)CC)C(=O)N[C@@H]([C@@H](C)CC)C(O)=O AAHSHTLISQUZJL-QSFUFRPTSA-N 0.000 description 2
- 102000004457 Granulocyte-Macrophage Colony-Stimulating Factor Human genes 0.000 description 2
- 108010017213 Granulocyte-Macrophage Colony-Stimulating Factor Proteins 0.000 description 2
- 102100028967 HLA class I histocompatibility antigen, alpha chain G Human genes 0.000 description 2
- 108010089211 HLA-A*25 antigen Proteins 0.000 description 2
- 108010078301 HLA-B*07:02 antigen Proteins 0.000 description 2
- 102220391613 HLA-B*2702 Human genes 0.000 description 2
- 108010061486 HLA-B27 Antigen Proteins 0.000 description 2
- 102000012153 HLA-B27 Antigen Human genes 0.000 description 2
- 108010033369 HLA-B57 antigen Proteins 0.000 description 2
- 108010026301 HLA-C*01:02 antigen Proteins 0.000 description 2
- 108010070768 HLA-C*03 antigen Proteins 0.000 description 2
- 108010057769 HLA-C*03:04 antigen Proteins 0.000 description 2
- 108010024164 HLA-G Antigens Proteins 0.000 description 2
- 241000700721 Hepatitis B virus Species 0.000 description 2
- 208000017604 Hodgkin disease Diseases 0.000 description 2
- 208000010747 Hodgkins lymphoma Diseases 0.000 description 2
- 101000578784 Homo sapiens Melanoma antigen recognized by T-cells 1 Proteins 0.000 description 2
- 101000880770 Homo sapiens Protein SSX2 Proteins 0.000 description 2
- 101001012157 Homo sapiens Receptor tyrosine-protein kinase erbB-2 Proteins 0.000 description 2
- 241000714260 Human T-lymphotropic virus 1 Species 0.000 description 2
- 241000701074 Human alphaherpesvirus 2 Species 0.000 description 2
- 101100048372 Human cytomegalovirus (strain AD169) H301 gene Proteins 0.000 description 2
- 101100048373 Human cytomegalovirus (strain Merlin) UL18 gene Proteins 0.000 description 2
- 101000767631 Human papillomavirus type 16 Protein E7 Proteins 0.000 description 2
- 102000004877 Insulin Human genes 0.000 description 2
- 108090001061 Insulin Proteins 0.000 description 2
- 108020004684 Internal Ribosome Entry Sites Proteins 0.000 description 2
- 102100031413 L-dopachrome tautomerase Human genes 0.000 description 2
- 101710093778 L-dopachrome tautomerase Proteins 0.000 description 2
- 241000712899 Lymphocytic choriomeningitis mammarenavirus Species 0.000 description 2
- 108010029973 Lymphocytic choriomeningitis virus glycoprotein peptide Proteins 0.000 description 2
- 241001465754 Metazoa Species 0.000 description 2
- 241000699660 Mus musculus Species 0.000 description 2
- 101800001020 Non-structural protein 4A Proteins 0.000 description 2
- 108091028043 Nucleic acid sequence Proteins 0.000 description 2
- 208000037581 Persistent Infection Diseases 0.000 description 2
- 108700003740 Poliovirus VP1 Proteins 0.000 description 2
- 101710149284 Protein SSX2 Proteins 0.000 description 2
- 102100037686 Protein SSX2 Human genes 0.000 description 2
- 108020004511 Recombinant DNA Proteins 0.000 description 2
- 206010070834 Sensitisation Diseases 0.000 description 2
- 101710173694 Short transient receptor potential channel 2 Proteins 0.000 description 2
- 230000005867 T cell response Effects 0.000 description 2
- 101150037769 TRX2 gene Proteins 0.000 description 2
- 208000035896 Twin-reversed arterial perfusion sequence Diseases 0.000 description 2
- 230000009471 action Effects 0.000 description 2
- 230000033289 adaptive immune response Effects 0.000 description 2
- 208000009956 adenocarcinoma Diseases 0.000 description 2
- 108010034034 alpha-1,6-mannosylglycoprotein beta 1,6-N-acetylglucosaminyltransferase Proteins 0.000 description 2
- 230000030741 antigen processing and presentation Effects 0.000 description 2
- 210000004899 c-terminal region Anatomy 0.000 description 2
- 230000015556 catabolic process Effects 0.000 description 2
- 239000003153 chemical reaction reagent Substances 0.000 description 2
- 239000011651 chromium Substances 0.000 description 2
- 238000010276 construction Methods 0.000 description 2
- 238000006731 degradation reaction Methods 0.000 description 2
- 239000012636 effector Substances 0.000 description 2
- 210000002472 endoplasmic reticulum Anatomy 0.000 description 2
- 238000010353 genetic engineering Methods 0.000 description 2
- 102000054766 genetic haplotypes Human genes 0.000 description 2
- 108010072094 gp100(280-288) melanoma antigen peptide Proteins 0.000 description 2
- 206010073071 hepatocellular carcinoma Diseases 0.000 description 2
- 230000001900 immune effect Effects 0.000 description 2
- 230000036039 immunity Effects 0.000 description 2
- 230000005847 immunogenicity Effects 0.000 description 2
- 238000011221 initial treatment Methods 0.000 description 2
- 229940125396 insulin Drugs 0.000 description 2
- 229940047124 interferons Drugs 0.000 description 2
- 108010003486 leucyl-leucyl-phenylalanyl-glycyl-tyrosyl-prolyl-valyl-tyrosyl-valine Proteins 0.000 description 2
- 208000032839 leukemia Diseases 0.000 description 2
- 208000014018 liver neoplasm Diseases 0.000 description 2
- 101710130522 mRNA export factor Proteins 0.000 description 2
- 239000002243 precursor Substances 0.000 description 2
- 230000026938 proteasomal ubiquitin-dependent protein catabolic process Effects 0.000 description 2
- 238000011160 research Methods 0.000 description 2
- 238000012552 review Methods 0.000 description 2
- 230000008313 sensitization Effects 0.000 description 2
- 241000894007 species Species 0.000 description 2
- 239000000126 substance Substances 0.000 description 2
- 238000006467 substitution reaction Methods 0.000 description 2
- 229940021747 therapeutic vaccine Drugs 0.000 description 2
- 230000005945 translocation Effects 0.000 description 2
- 230000032258 transport Effects 0.000 description 2
- 108010059061 tyrosyl-leucyl-asparagyl-lysyl-isoleucyl-glutaminyl-asparagyl-seryl-leucine Proteins 0.000 description 2
- VPOQHEDQPXVVEK-PUYUYYSSSA-N (2r)-2-[[(2s,3s)-2-[[(2s)-1-[(2r)-2-[[(2s)-2-[[(2s,3s)-2-[[2-[[(2s)-2-[[(2s,3r)-2-amino-3-hydroxybutanoyl]amino]-4-methylpentanoyl]amino]acetyl]amino]-3-methylpentanoyl]amino]-3-methylbutanoyl]amino]-3-sulfanylpropanoyl]pyrrolidine-2-carbonyl]amino]-3-met Chemical compound C[C@@H](O)[C@H](N)C(=O)N[C@@H](CC(C)C)C(=O)NCC(=O)N[C@@H]([C@@H](C)CC)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H](CS)C(=O)N1CCC[C@H]1C(=O)N[C@@H]([C@@H](C)CC)C(=O)N[C@@H](CS)C(O)=O VPOQHEDQPXVVEK-PUYUYYSSSA-N 0.000 description 1
- BRPMXFSTKXXNHF-IUCAKERBSA-N (2s)-1-[2-[[(2s)-pyrrolidine-2-carbonyl]amino]acetyl]pyrrolidine-2-carboxylic acid Chemical compound OC(=O)[C@@H]1CCCN1C(=O)CNC(=O)[C@H]1NCCC1 BRPMXFSTKXXNHF-IUCAKERBSA-N 0.000 description 1
- JVJGCCBAOOWGEO-RUTPOYCXSA-N (2s)-2-[[(2s)-2-[[(2s)-2-[[(2s)-2-[[(2s)-4-amino-2-[[(2s,3s)-2-[[(2s,3s)-2-[[(2s)-2-azaniumyl-3-hydroxypropanoyl]amino]-3-methylpentanoyl]amino]-3-methylpentanoyl]amino]-4-oxobutanoyl]amino]-3-phenylpropanoyl]amino]-4-carboxylatobutanoyl]amino]-6-azaniumy Chemical compound OC[C@H](N)C(=O)N[C@@H]([C@@H](C)CC)C(=O)N[C@@H]([C@@H](C)CC)C(=O)N[C@@H](CC(N)=O)C(=O)N[C@H](C(=O)N[C@@H](CCC(O)=O)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CC(C)C)C(O)=O)CC1=CC=CC=C1 JVJGCCBAOOWGEO-RUTPOYCXSA-N 0.000 description 1
- HVUSPTXVKJVJLC-KFFSJVQZSA-N (2s,3s)-2-[[(2r)-2-[[(2s)-2-[[(2s)-2-[[(2s)-2-[[(2s)-1-[(2s)-2-[[(2s)-2-[[(2s)-2-aminopropanoyl]amino]-4-methylpentanoyl]amino]-4-methylsulfanylbutanoyl]pyrrolidine-2-carbonyl]amino]-4-methylpentanoyl]amino]-3-(4-hydroxyphenyl)propanoyl]amino]propanoyl]am Chemical compound C([C@@H](C(=O)N[C@@H](C)C(=O)N[C@@H](CS)C(=O)N[C@@H]([C@@H](C)CC)C(O)=O)NC(=O)[C@H](CC(C)C)NC(=O)[C@H]1N(CCC1)C(=O)[C@H](CCSC)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](C)N)C1=CC=C(O)C=C1 HVUSPTXVKJVJLC-KFFSJVQZSA-N 0.000 description 1
- 108091032973 (ribonucleotides)n+m Proteins 0.000 description 1
- GHCZTIFQWKKGSB-UHFFFAOYSA-N 2-hydroxypropane-1,2,3-tricarboxylic acid;phosphoric acid Chemical compound OP(O)(O)=O.OC(=O)CC(O)(C(O)=O)CC(O)=O GHCZTIFQWKKGSB-UHFFFAOYSA-N 0.000 description 1
- 102100026936 2-oxoglutarate dehydrogenase, mitochondrial Human genes 0.000 description 1
- WEVYNIUIFUYDGI-UHFFFAOYSA-N 3-[6-[4-(trifluoromethoxy)anilino]-4-pyrimidinyl]benzamide Chemical compound NC(=O)C1=CC=CC(C=2N=CN=C(NC=3C=CC(OC(F)(F)F)=CC=3)C=2)=C1 WEVYNIUIFUYDGI-UHFFFAOYSA-N 0.000 description 1
- 102100030310 5,6-dihydroxyindole-2-carboxylic acid oxidase Human genes 0.000 description 1
- 101710163881 5,6-dihydroxyindole-2-carboxylic acid oxidase Proteins 0.000 description 1
- 208000024893 Acute lymphoblastic leukemia Diseases 0.000 description 1
- 208000014697 Acute lymphocytic leukaemia Diseases 0.000 description 1
- 208000031261 Acute myeloid leukaemia Diseases 0.000 description 1
- 108010087905 Adenovirus E1B Proteins Proteins 0.000 description 1
- 108010027410 Adenovirus E3 Proteins Proteins 0.000 description 1
- LGFCAXJBAZESCF-ACZMJKKPSA-N Ala-Gln-Ala Chemical compound [H]N[C@@H](C)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](C)C(O)=O LGFCAXJBAZESCF-ACZMJKKPSA-N 0.000 description 1
- WUHJHHGYVVJMQE-BJDJZHNGSA-N Ala-Leu-Ile Chemical compound [H]N[C@@H](C)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H]([C@@H](C)CC)C(O)=O WUHJHHGYVVJMQE-BJDJZHNGSA-N 0.000 description 1
- UJJUHXAJSRHWFZ-DCAQKATOSA-N Ala-Leu-Val Chemical compound [H]N[C@@H](C)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C(C)C)C(O)=O UJJUHXAJSRHWFZ-DCAQKATOSA-N 0.000 description 1
- OLVCTPPSXNRGKV-GUBZILKMSA-N Ala-Pro-Pro Chemical compound C[C@H](N)C(=O)N1CCC[C@H]1C(=O)N1[C@H](C(O)=O)CCC1 OLVCTPPSXNRGKV-GUBZILKMSA-N 0.000 description 1
- 108700028369 Alleles Proteins 0.000 description 1
- 201000003076 Angiosarcoma Diseases 0.000 description 1
- IIABBYGHLYWVOS-FXQIFTODSA-N Arg-Asn-Ser Chemical compound [H]N[C@@H](CCCNC(N)=N)C(=O)N[C@@H](CC(N)=O)C(=O)N[C@@H](CO)C(O)=O IIABBYGHLYWVOS-FXQIFTODSA-N 0.000 description 1
- QCVXMEHGFUMKCO-YUMQZZPRSA-N Asp-Gly-Leu Chemical compound CC(C)C[C@@H](C(O)=O)NC(=O)CNC(=O)[C@@H](N)CC(O)=O QCVXMEHGFUMKCO-YUMQZZPRSA-N 0.000 description 1
- 206010003571 Astrocytoma Diseases 0.000 description 1
- 102100035526 B melanoma antigen 1 Human genes 0.000 description 1
- 208000010839 B-cell chronic lymphocytic leukemia Diseases 0.000 description 1
- 101150009389 BZLF1 gene Proteins 0.000 description 1
- 206010004146 Basal cell carcinoma Diseases 0.000 description 1
- 206010004593 Bile duct cancer Diseases 0.000 description 1
- 206010005003 Bladder cancer Diseases 0.000 description 1
- 208000003174 Brain Neoplasms Diseases 0.000 description 1
- 206010006187 Breast cancer Diseases 0.000 description 1
- 208000026310 Breast neoplasm Diseases 0.000 description 1
- 241000589562 Brucella Species 0.000 description 1
- 101100441244 Caenorhabditis elegans csp-1 gene Proteins 0.000 description 1
- 102100029968 Calreticulin Human genes 0.000 description 1
- 108090000549 Calreticulin Proteins 0.000 description 1
- 101710132601 Capsid protein Proteins 0.000 description 1
- 102000014914 Carrier Proteins Human genes 0.000 description 1
- 108010078791 Carrier Proteins Proteins 0.000 description 1
- 206010008342 Cervix carcinoma Diseases 0.000 description 1
- 241000606161 Chlamydia Species 0.000 description 1
- 208000005243 Chondrosarcoma Diseases 0.000 description 1
- 201000009047 Chordoma Diseases 0.000 description 1
- 208000006332 Choriocarcinoma Diseases 0.000 description 1
- VYZAMTAEIAYCRO-UHFFFAOYSA-N Chromium Chemical compound [Cr] VYZAMTAEIAYCRO-UHFFFAOYSA-N 0.000 description 1
- 101710094648 Coat protein Proteins 0.000 description 1
- 108020004705 Codon Proteins 0.000 description 1
- 206010009944 Colon cancer Diseases 0.000 description 1
- 241001445332 Coxiella <snail> Species 0.000 description 1
- 208000009798 Craniopharyngioma Diseases 0.000 description 1
- 241001146209 Curio rowleyanus Species 0.000 description 1
- 102000013701 Cyclin-Dependent Kinase 4 Human genes 0.000 description 1
- 108010025464 Cyclin-Dependent Kinase 4 Proteins 0.000 description 1
- 102000004127 Cytokines Human genes 0.000 description 1
- 108090000695 Cytokines Proteins 0.000 description 1
- 102000053602 DNA Human genes 0.000 description 1
- 108010041986 DNA Vaccines Proteins 0.000 description 1
- 238000001712 DNA sequencing Methods 0.000 description 1
- 229940021995 DNA vaccine Drugs 0.000 description 1
- 102000004163 DNA-directed RNA polymerases Human genes 0.000 description 1
- 108090000626 DNA-directed RNA polymerases Proteins 0.000 description 1
- 108050002772 E3 ubiquitin-protein ligase Mdm2 Proteins 0.000 description 1
- 102000012199 E3 ubiquitin-protein ligase Mdm2 Human genes 0.000 description 1
- 108010031763 E474 peptide Proteins 0.000 description 1
- KCXVZYZYPLLWCC-UHFFFAOYSA-N EDTA Chemical compound OC(=O)CN(CC(O)=O)CCN(CC(O)=O)CC(O)=O KCXVZYZYPLLWCC-UHFFFAOYSA-N 0.000 description 1
- 238000011510 Elispot assay Methods 0.000 description 1
- 201000009051 Embryonal Carcinoma Diseases 0.000 description 1
- 241000710188 Encephalomyocarditis virus Species 0.000 description 1
- 206010014967 Ependymoma Diseases 0.000 description 1
- 208000031637 Erythroblastic Acute Leukemia Diseases 0.000 description 1
- 208000036566 Erythroleukaemia Diseases 0.000 description 1
- 101000738180 Euglena gracilis Chaperonin CPN60, mitochondrial Proteins 0.000 description 1
- 208000006168 Ewing Sarcoma Diseases 0.000 description 1
- 201000008808 Fibrosarcoma Diseases 0.000 description 1
- 241000233866 Fungi Species 0.000 description 1
- 102100039717 G antigen 1 Human genes 0.000 description 1
- 101710113436 GTPase KRas Proteins 0.000 description 1
- 108700028146 Genetic Enhancer Elements Proteins 0.000 description 1
- 208000032612 Glial tumor Diseases 0.000 description 1
- 206010018338 Glioma Diseases 0.000 description 1
- YJIUYQKQBBQYHZ-ACZMJKKPSA-N Gln-Ala-Ala Chemical compound [H]N[C@@H](CCC(N)=O)C(=O)N[C@@H](C)C(=O)N[C@@H](C)C(O)=O YJIUYQKQBBQYHZ-ACZMJKKPSA-N 0.000 description 1
- IWUFOVSLWADEJC-AVGNSLFASA-N Gln-His-Leu Chemical compound [H]N[C@@H](CCC(N)=O)C(=O)N[C@@H](CC1=CNC=N1)C(=O)N[C@@H](CC(C)C)C(O)=O IWUFOVSLWADEJC-AVGNSLFASA-N 0.000 description 1
- VYOILACOFPPNQH-UMNHJUIQSA-N Gln-Val-Pro Chemical compound CC(C)[C@@H](C(=O)N1CCC[C@@H]1C(=O)O)NC(=O)[C@H](CCC(=O)N)N VYOILACOFPPNQH-UMNHJUIQSA-N 0.000 description 1
- WZZSKAJIHTUUSG-ACZMJKKPSA-N Glu-Ala-Asp Chemical compound OC(=O)C[C@@H](C(O)=O)NC(=O)[C@H](C)NC(=O)[C@@H](N)CCC(O)=O WZZSKAJIHTUUSG-ACZMJKKPSA-N 0.000 description 1
- ITYRYNUZHPNCIK-GUBZILKMSA-N Glu-Ala-Leu Chemical compound [H]N[C@@H](CCC(O)=O)C(=O)N[C@@H](C)C(=O)N[C@@H](CC(C)C)C(O)=O ITYRYNUZHPNCIK-GUBZILKMSA-N 0.000 description 1
- LKOAAMXDJGEYMS-ZPFDUUQYSA-N Glu-Met-Ile Chemical compound [H]N[C@@H](CCC(O)=O)C(=O)N[C@@H](CCSC)C(=O)N[C@@H]([C@@H](C)CC)C(O)=O LKOAAMXDJGEYMS-ZPFDUUQYSA-N 0.000 description 1
- CAQXJMUDOLSBPF-SUSMZKCASA-N Glu-Thr-Thr Chemical compound [H]N[C@@H](CCC(O)=O)C(=O)N[C@@H]([C@@H](C)O)C(=O)N[C@@H]([C@@H](C)O)C(O)=O CAQXJMUDOLSBPF-SUSMZKCASA-N 0.000 description 1
- UESJMAMHDLEHGM-NHCYSSNCSA-N Gly-Ile-Leu Chemical compound NCC(=O)N[C@@H]([C@@H](C)CC)C(=O)N[C@@H](CC(C)C)C(O)=O UESJMAMHDLEHGM-NHCYSSNCSA-N 0.000 description 1
- UHPAZODVFFYEEL-QWRGUYRKSA-N Gly-Leu-Leu Chemical compound CC(C)C[C@@H](C(O)=O)NC(=O)[C@H](CC(C)C)NC(=O)CN UHPAZODVFFYEEL-QWRGUYRKSA-N 0.000 description 1
- 102100021181 Golgi phosphoprotein 3 Human genes 0.000 description 1
- 108010058155 HA (255-262) Proteins 0.000 description 1
- 108010073434 HLA-A*02:09 antigen Proteins 0.000 description 1
- 108010080347 HLA-A*26 antigen Proteins 0.000 description 1
- 108010035452 HLA-A1 Antigen Proteins 0.000 description 1
- 108010087017 HLA-B14 Antigen Proteins 0.000 description 1
- 108010013698 HLA-B17 antigen Proteins 0.000 description 1
- 108010070087 HLA-B37 Antigen Proteins 0.000 description 1
- 108010014398 HLA-B42 antigen Proteins 0.000 description 1
- 108010059045 HLA-C*06 antigen Proteins 0.000 description 1
- 108010059421 HLA-C*16 antigen Proteins 0.000 description 1
- 102000006354 HLA-DR Antigens Human genes 0.000 description 1
- 108010058597 HLA-DR Antigens Proteins 0.000 description 1
- 208000001258 Hemangiosarcoma Diseases 0.000 description 1
- 241000711549 Hepacivirus C Species 0.000 description 1
- 208000037262 Hepatitis delta Diseases 0.000 description 1
- 241000724709 Hepatitis delta virus Species 0.000 description 1
- SVVULKPWDBIPCO-BZSNNMDCSA-N His-Phe-Leu Chemical compound [H]N[C@@H](CC1=CNC=N1)C(=O)N[C@@H](CC1=CC=CC=C1)C(=O)N[C@@H](CC(C)C)C(O)=O SVVULKPWDBIPCO-BZSNNMDCSA-N 0.000 description 1
- KRBMQYPTDYSENE-BQBZGAKWSA-N His-Ser Chemical compound OC[C@@H](C(O)=O)NC(=O)[C@@H](N)CC1=CNC=N1 KRBMQYPTDYSENE-BQBZGAKWSA-N 0.000 description 1
- FFKJUTZARGRVTH-KKUMJFAQSA-N His-Ser-Tyr Chemical compound [H]N[C@@H](CC1=CNC=N1)C(=O)N[C@@H](CO)C(=O)N[C@@H](CC1=CC=C(O)C=C1)C(O)=O FFKJUTZARGRVTH-KKUMJFAQSA-N 0.000 description 1
- 241000282412 Homo Species 0.000 description 1
- 101000982656 Homo sapiens 2-oxoglutarate dehydrogenase, mitochondrial Proteins 0.000 description 1
- 101000883686 Homo sapiens 60 kDa heat shock protein, mitochondrial Proteins 0.000 description 1
- 101000874316 Homo sapiens B melanoma antigen 1 Proteins 0.000 description 1
- 101000738354 Homo sapiens CD9 antigen Proteins 0.000 description 1
- 101000886137 Homo sapiens G antigen 1 Proteins 0.000 description 1
- 101000887490 Homo sapiens Guanine nucleotide-binding protein G(z) subunit alpha Proteins 0.000 description 1
- 101000986086 Homo sapiens HLA class I histocompatibility antigen, A alpha chain Proteins 0.000 description 1
- 101001088879 Homo sapiens Lysine-specific demethylase 5D Proteins 0.000 description 1
- 101000620359 Homo sapiens Melanocyte protein PMEL Proteins 0.000 description 1
- 101001005720 Homo sapiens Melanoma-associated antigen 4 Proteins 0.000 description 1
- 101000854908 Homo sapiens WD repeat-containing protein 11 Proteins 0.000 description 1
- 108010070875 Human Immunodeficiency Virus tat Gene Products Proteins 0.000 description 1
- 241000714259 Human T-lymphotropic virus 2 Species 0.000 description 1
- 241000193096 Human adenovirus B3 Species 0.000 description 1
- 241000701085 Human alphaherpesvirus 3 Species 0.000 description 1
- 101100427508 Human cytomegalovirus (strain AD169) UL39 gene Proteins 0.000 description 1
- 241000701044 Human gammaherpesvirus 4 Species 0.000 description 1
- 241000701027 Human herpesvirus 6 Species 0.000 description 1
- 241000701828 Human papillomavirus type 11 Species 0.000 description 1
- 241000702617 Human parvovirus B19 Species 0.000 description 1
- 241000829111 Human polyomavirus 1 Species 0.000 description 1
- PHRWFSFCNJPWRO-PPCPHDFISA-N Ile-Leu-Thr Chemical compound CC[C@H](C)[C@@H](C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H]([C@@H](C)O)C(=O)O)N PHRWFSFCNJPWRO-PPCPHDFISA-N 0.000 description 1
- 108060003951 Immunoglobulin Proteins 0.000 description 1
- 108010030506 Integrin alpha6beta4 Proteins 0.000 description 1
- 101150008942 J gene Proteins 0.000 description 1
- 241000701460 JC polyomavirus Species 0.000 description 1
- IBMVEYRWAWIOTN-UHFFFAOYSA-N L-Leucyl-L-Arginyl-L-Proline Natural products CC(C)CC(N)C(=O)NC(CCCN=C(N)N)C(=O)N1CCCC1C(O)=O IBMVEYRWAWIOTN-UHFFFAOYSA-N 0.000 description 1
- QNAYBMKLOCPYGJ-REOHCLBHSA-N L-alanine Chemical compound C[C@H](N)C(O)=O QNAYBMKLOCPYGJ-REOHCLBHSA-N 0.000 description 1
- 241000589248 Legionella Species 0.000 description 1
- 208000007764 Legionnaires' Disease Diseases 0.000 description 1
- 208000018142 Leiomyosarcoma Diseases 0.000 description 1
- 241000222722 Leishmania <genus> Species 0.000 description 1
- 241001142635 Lema Species 0.000 description 1
- IBMVEYRWAWIOTN-RWMBFGLXSA-N Leu-Arg-Pro Chemical compound CC(C)C[C@H](N)C(=O)N[C@@H](CCCN=C(N)N)C(=O)N1CCC[C@@H]1C(O)=O IBMVEYRWAWIOTN-RWMBFGLXSA-N 0.000 description 1
- LESXFEZIFXFIQR-LURJTMIESA-N Leu-Gly Chemical compound CC(C)C[C@H](N)C(=O)NCC(O)=O LESXFEZIFXFIQR-LURJTMIESA-N 0.000 description 1
- LCPYQJIKPJDLLB-UWVGGRQHSA-N Leu-Leu Chemical compound CC(C)C[C@H](N)C(=O)N[C@H](C(O)=O)CC(C)C LCPYQJIKPJDLLB-UWVGGRQHSA-N 0.000 description 1
- YOKVEHGYYQEQOP-QWRGUYRKSA-N Leu-Leu-Gly Chemical compound CC(C)C[C@H](N)C(=O)N[C@@H](CC(C)C)C(=O)NCC(O)=O YOKVEHGYYQEQOP-QWRGUYRKSA-N 0.000 description 1
- MDSUKZSLOATHMH-IUCAKERBSA-N Leu-Val Chemical compound CC(C)C[C@H]([NH3+])C(=O)N[C@@H](C(C)C)C([O-])=O MDSUKZSLOATHMH-IUCAKERBSA-N 0.000 description 1
- 206010024305 Leukaemia monocytic Diseases 0.000 description 1
- 241000186781 Listeria Species 0.000 description 1
- 206010058467 Lung neoplasm malignant Diseases 0.000 description 1
- 208000031422 Lymphocytic Chronic B-Cell Leukemia Diseases 0.000 description 1
- 206010025323 Lymphomas Diseases 0.000 description 1
- DTUZCYRNEJDKSR-NHCYSSNCSA-N Lys-Gly-Ile Chemical compound CC[C@H](C)[C@@H](C(O)=O)NC(=O)CNC(=O)[C@@H](N)CCCCN DTUZCYRNEJDKSR-NHCYSSNCSA-N 0.000 description 1
- AIRZWUMAHCDDHR-KKUMJFAQSA-N Lys-Leu-Leu Chemical compound [H]N[C@@H](CCCCN)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CC(C)C)C(O)=O AIRZWUMAHCDDHR-KKUMJFAQSA-N 0.000 description 1
- 102100033143 Lysine-specific demethylase 5D Human genes 0.000 description 1
- 102000016200 MART-1 Antigen Human genes 0.000 description 1
- 241000282553 Macaca Species 0.000 description 1
- 241000710118 Maize chlorotic mottle virus Species 0.000 description 1
- 101710125418 Major capsid protein Proteins 0.000 description 1
- 241000712079 Measles morbillivirus Species 0.000 description 1
- 208000007054 Medullary Carcinoma Diseases 0.000 description 1
- 208000000172 Medulloblastoma Diseases 0.000 description 1
- 102100025077 Melanoma-associated antigen 4 Human genes 0.000 description 1
- 206010027406 Mesothelioma Diseases 0.000 description 1
- 208000034578 Multiple myelomas Diseases 0.000 description 1
- 101100263241 Mus musculus Uty gene Proteins 0.000 description 1
- 101100264174 Mus musculus Xiap gene Proteins 0.000 description 1
- 241000186359 Mycobacterium Species 0.000 description 1
- 208000033776 Myeloid Acute Leukemia Diseases 0.000 description 1
- 102000003505 Myosin Human genes 0.000 description 1
- 108060008487 Myosin Proteins 0.000 description 1
- MDSUKZSLOATHMH-UHFFFAOYSA-N N-L-leucyl-L-valine Natural products CC(C)CC(N)C(=O)NC(C(C)C)C(O)=O MDSUKZSLOATHMH-UHFFFAOYSA-N 0.000 description 1
- 206010029260 Neuroblastoma Diseases 0.000 description 1
- 101710141454 Nucleoprotein Proteins 0.000 description 1
- 201000010133 Oligodendroglioma Diseases 0.000 description 1
- 108010058846 Ovalbumin Proteins 0.000 description 1
- 206010033128 Ovarian cancer Diseases 0.000 description 1
- 206010061535 Ovarian neoplasm Diseases 0.000 description 1
- 108010036616 P18-I10 peptide Proteins 0.000 description 1
- 229920006706 PC-C Polymers 0.000 description 1
- 241000194105 Paenibacillus polymyxa Species 0.000 description 1
- 101100161152 Pan troglodytes Patr-A gene Proteins 0.000 description 1
- 206010061902 Pancreatic neoplasm Diseases 0.000 description 1
- 241001631646 Papillomaviridae Species 0.000 description 1
- 241001504519 Papio ursinus Species 0.000 description 1
- 101150098008 Patr-A gene Proteins 0.000 description 1
- 108010088535 Pep-1 peptide Proteins 0.000 description 1
- LWPMGKSZPKFKJD-DZKIICNBSA-N Phe-Glu-Val Chemical compound [H]N[C@@H](CC1=CC=CC=C1)C(=O)N[C@@H](CCC(O)=O)C(=O)N[C@@H](C(C)C)C(O)=O LWPMGKSZPKFKJD-DZKIICNBSA-N 0.000 description 1
- FGWUALWGCZJQDJ-URLPEUOOSA-N Phe-Thr-Ile Chemical compound [H]N[C@@H](CC1=CC=CC=C1)C(=O)N[C@@H]([C@@H](C)O)C(=O)N[C@@H]([C@@H](C)CC)C(O)=O FGWUALWGCZJQDJ-URLPEUOOSA-N 0.000 description 1
- VDTYRPWRWRCROL-UFYCRDLUSA-N Phe-Val-Phe Chemical compound C([C@H](N)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H](CC=1C=CC=CC=1)C(O)=O)C1=CC=CC=C1 VDTYRPWRWRCROL-UFYCRDLUSA-N 0.000 description 1
- 208000007641 Pinealoma Diseases 0.000 description 1
- 206010035226 Plasma cell myeloma Diseases 0.000 description 1
- 241000224016 Plasmodium Species 0.000 description 1
- 208000006664 Precursor Cell Lymphoblastic Leukemia-Lymphoma Diseases 0.000 description 1
- DCHQYSOGURGJST-FJXKBIBVSA-N Pro-Thr-Gly Chemical compound [H]N1CCC[C@H]1C(=O)N[C@@H]([C@@H](C)O)C(=O)NCC(O)=O DCHQYSOGURGJST-FJXKBIBVSA-N 0.000 description 1
- 101710083689 Probable capsid protein Proteins 0.000 description 1
- 206010060862 Prostate cancer Diseases 0.000 description 1
- 208000000236 Prostatic Neoplasms Diseases 0.000 description 1
- 101150093191 RIR1 gene Proteins 0.000 description 1
- 206010037742 Rabies Diseases 0.000 description 1
- 101710100968 Receptor tyrosine-protein kinase erbB-2 Proteins 0.000 description 1
- 208000006265 Renal cell carcinoma Diseases 0.000 description 1
- 201000000582 Retinoblastoma Diseases 0.000 description 1
- 241000606701 Rickettsia Species 0.000 description 1
- 108700003736 Rotavirus VP3 Proteins 0.000 description 1
- 108700031314 Rotavirus VP6 Proteins 0.000 description 1
- 108700012261 Rotavirus VP7 Proteins 0.000 description 1
- 241000710799 Rubella virus Species 0.000 description 1
- 240000004808 Saccharomyces cerevisiae Species 0.000 description 1
- 241000607142 Salmonella Species 0.000 description 1
- 206010039491 Sarcoma Diseases 0.000 description 1
- 201000010208 Seminoma Diseases 0.000 description 1
- HVKMTOIAYDOJPL-NRPADANISA-N Ser-Gln-Val Chemical compound [H]N[C@@H](CO)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](C(C)C)C(O)=O HVKMTOIAYDOJPL-NRPADANISA-N 0.000 description 1
- 101710173693 Short transient receptor potential channel 1 Proteins 0.000 description 1
- 208000005718 Stomach Neoplasms Diseases 0.000 description 1
- 241000187399 Streptomyces lincolnensis Species 0.000 description 1
- 101710143177 Synaptonemal complex protein 1 Proteins 0.000 description 1
- 102100036234 Synaptonemal complex protein 1 Human genes 0.000 description 1
- 230000024932 T cell mediated immunity Effects 0.000 description 1
- 102100033130 T-box transcription factor T Human genes 0.000 description 1
- 101710086566 T-box transcription factor T Proteins 0.000 description 1
- 108020005038 Terminator Codon Proteins 0.000 description 1
- 208000024313 Testicular Neoplasms Diseases 0.000 description 1
- BQBCIBCLXBKYHW-CSMHCCOUSA-N Thr-Leu Chemical compound CC(C)C[C@@H](C([O-])=O)NC(=O)[C@@H]([NH3+])[C@@H](C)O BQBCIBCLXBKYHW-CSMHCCOUSA-N 0.000 description 1
- CKHWEVXPLJBEOZ-VQVTYTSYSA-N Thr-Val Chemical compound CC(C)[C@@H](C([O-])=O)NC(=O)[C@@H]([NH3+])[C@@H](C)O CKHWEVXPLJBEOZ-VQVTYTSYSA-N 0.000 description 1
- 241000223996 Toxoplasma Species 0.000 description 1
- LVTKHGUGBGNBPL-UHFFFAOYSA-N Trp-P-1 Chemical compound N1C2=CC=CC=C2C2=C1C(C)=C(N)N=C2C LVTKHGUGBGNBPL-UHFFFAOYSA-N 0.000 description 1
- KSCVLGXNQXKUAR-JYJNAYRXSA-N Tyr-Leu-Glu Chemical compound [H]N[C@@H](CC1=CC=C(O)C=C1)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CCC(O)=O)C(O)=O KSCVLGXNQXKUAR-JYJNAYRXSA-N 0.000 description 1
- 102100039094 Tyrosinase Human genes 0.000 description 1
- 101150066971 UL49 gene Proteins 0.000 description 1
- 108090000848 Ubiquitin Proteins 0.000 description 1
- 102000044159 Ubiquitin Human genes 0.000 description 1
- 208000006105 Uterine Cervical Neoplasms Diseases 0.000 description 1
- FTKXYXACXYOHND-XUXIUFHCSA-N Val-Ile-Leu Chemical compound CC(C)[C@H](N)C(=O)N[C@@H]([C@@H](C)CC)C(=O)N[C@@H](CC(C)C)C(O)=O FTKXYXACXYOHND-XUXIUFHCSA-N 0.000 description 1
- CEKSLIVSNNGOKH-KZVJFYERSA-N Val-Thr-Ala Chemical compound C[C@H]([C@@H](C(=O)N[C@@H](C)C(=O)O)NC(=O)[C@H](C(C)C)N)O CEKSLIVSNNGOKH-KZVJFYERSA-N 0.000 description 1
- 208000014070 Vestibular schwannoma Diseases 0.000 description 1
- 102100020705 WD repeat-containing protein 11 Human genes 0.000 description 1
- 208000033559 Waldenström macroglobulinemia Diseases 0.000 description 1
- 208000008383 Wilms tumor Diseases 0.000 description 1
- 239000002253 acid Substances 0.000 description 1
- 208000004064 acoustic neuroma Diseases 0.000 description 1
- 208000017733 acquired polycythemia vera Diseases 0.000 description 1
- 208000021841 acute erythroid leukemia Diseases 0.000 description 1
- 239000002671 adjuvant Substances 0.000 description 1
- 235000004279 alanine Nutrition 0.000 description 1
- 230000003321 amplification Effects 0.000 description 1
- 238000000137 annealing Methods 0.000 description 1
- 230000005809 anti-tumor immunity Effects 0.000 description 1
- 238000013459 approach Methods 0.000 description 1
- 108010093581 aspartyl-proline Proteins 0.000 description 1
- 239000011324 bead Substances 0.000 description 1
- 201000007180 bile duct carcinoma Diseases 0.000 description 1
- 201000001531 bladder carcinoma Diseases 0.000 description 1
- 210000004369 blood Anatomy 0.000 description 1
- 239000008280 blood Substances 0.000 description 1
- 108010006025 bovine growth hormone Proteins 0.000 description 1
- 208000003362 bronchogenic carcinoma Diseases 0.000 description 1
- 230000003197 catalytic effect Effects 0.000 description 1
- 210000004671 cell-free system Anatomy 0.000 description 1
- 230000036755 cellular response Effects 0.000 description 1
- 201000010881 cervical cancer Diseases 0.000 description 1
- 229910052804 chromium Inorganic materials 0.000 description 1
- 208000024207 chronic leukemia Diseases 0.000 description 1
- 208000032852 chronic lymphocytic leukemia Diseases 0.000 description 1
- 230000000052 comparative effect Effects 0.000 description 1
- 238000013270 controlled release Methods 0.000 description 1
- 230000000139 costimulatory effect Effects 0.000 description 1
- LXWYCLOUQZZDBD-LIYNQYRNSA-N csfv Chemical compound C([C@H](NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CCC(O)=O)NC(=O)[C@H](CC(C)C)NC(=O)[C@@H](N)[C@@H](C)CC)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CC=1C=CC=CC=1)C(=O)N[C@@H](CCCNC(N)=N)C(=O)N[C@@H](CC(O)=O)C(=O)N[C@@H](CC(N)=O)C(=O)N[C@@H]([C@@H](C)CC)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CO)C(=O)N[C@@H](CO)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H](CCCNC(N)=N)C(=O)N[C@@H](CCC(O)=O)C(O)=O)C1=CC=C(O)C=C1 LXWYCLOUQZZDBD-LIYNQYRNSA-N 0.000 description 1
- 208000002445 cystadenocarcinoma Diseases 0.000 description 1
- 230000016396 cytokine production Effects 0.000 description 1
- 210000000805 cytoplasm Anatomy 0.000 description 1
- 210000000172 cytosol Anatomy 0.000 description 1
- 230000006378 damage Effects 0.000 description 1
- 230000001419 dependent effect Effects 0.000 description 1
- 238000001514 detection method Methods 0.000 description 1
- 238000011161 development Methods 0.000 description 1
- 230000008034 disappearance Effects 0.000 description 1
- 238000012377 drug delivery Methods 0.000 description 1
- 238000005516 engineering process Methods 0.000 description 1
- 239000003623 enhancer Substances 0.000 description 1
- 230000002255 enzymatic effect Effects 0.000 description 1
- 238000003114 enzyme-linked immunosorbent spot assay Methods 0.000 description 1
- 208000037828 epithelial carcinoma Diseases 0.000 description 1
- 235000019441 ethanol Nutrition 0.000 description 1
- 230000004927 fusion Effects 0.000 description 1
- 206010017758 gastric cancer Diseases 0.000 description 1
- 238000001415 gene therapy Methods 0.000 description 1
- 230000002068 genetic effect Effects 0.000 description 1
- 108010051667 glutamyl-glutamyl-asparagyl-leucyl-leucyl-aspartyl-phenylalanyl-valyl-arginyl-phenylalanine Proteins 0.000 description 1
- 108010050848 glycylleucine Proteins 0.000 description 1
- 108010014242 gp100(17-25) peptide Proteins 0.000 description 1
- 208000025750 heavy chain disease Diseases 0.000 description 1
- 201000002222 hemangioblastoma Diseases 0.000 description 1
- 108010018006 histidylserine Proteins 0.000 description 1
- 102000043530 human CD9 Human genes 0.000 description 1
- 102000052301 human GNAZ Human genes 0.000 description 1
- 238000009396 hybridization Methods 0.000 description 1
- 230000036737 immune function Effects 0.000 description 1
- 102000018358 immunoglobulin Human genes 0.000 description 1
- 230000002434 immunopotentiative effect Effects 0.000 description 1
- 230000001024 immunotherapeutic effect Effects 0.000 description 1
- 238000009169 immunotherapy Methods 0.000 description 1
- 238000005462 in vivo assay Methods 0.000 description 1
- 238000010348 incorporation Methods 0.000 description 1
- 230000006698 induction Effects 0.000 description 1
- 230000002458 infectious effect Effects 0.000 description 1
- 230000001524 infective effect Effects 0.000 description 1
- 230000015788 innate immune response Effects 0.000 description 1
- 239000000543 intermediate Substances 0.000 description 1
- 229930027917 kanamycin Natural products 0.000 description 1
- SBUJHOSQTJFQJX-NOAMYHISSA-N kanamycin Chemical compound O[C@@H]1[C@@H](O)[C@H](O)[C@@H](CN)O[C@@H]1O[C@H]1[C@H](O)[C@@H](O[C@@H]2[C@@H]([C@@H](N)[C@H](O)[C@@H](CO)O2)O)[C@H](N)C[C@@H]1N SBUJHOSQTJFQJX-NOAMYHISSA-N 0.000 description 1
- 229960000318 kanamycin Drugs 0.000 description 1
- 229930182823 kanamycin A Natural products 0.000 description 1
- 210000003734 kidney Anatomy 0.000 description 1
- 108010091798 leucylleucine Proteins 0.000 description 1
- 210000000265 leukocyte Anatomy 0.000 description 1
- 206010024627 liposarcoma Diseases 0.000 description 1
- 239000002502 liposome Substances 0.000 description 1
- 201000007270 liver cancer Diseases 0.000 description 1
- 201000005296 lung carcinoma Diseases 0.000 description 1
- 208000037829 lymphangioendotheliosarcoma Diseases 0.000 description 1
- 208000012804 lymphangiosarcoma Diseases 0.000 description 1
- 108010031238 lymphocytic choriomeningitis virus nucleoprotein peptide 118-126 Proteins 0.000 description 1
- 230000000527 lymphocytic effect Effects 0.000 description 1
- 230000002101 lytic effect Effects 0.000 description 1
- 210000002540 macrophage Anatomy 0.000 description 1
- 230000014759 maintenance of location Effects 0.000 description 1
- 208000015486 malignant pancreatic neoplasm Diseases 0.000 description 1
- 208000023356 medullary thyroid gland carcinoma Diseases 0.000 description 1
- 229940115256 melanoma vaccine Drugs 0.000 description 1
- 206010027191 meningioma Diseases 0.000 description 1
- 201000006894 monocytic leukemia Diseases 0.000 description 1
- 208000001611 myxosarcoma Diseases 0.000 description 1
- PUPNJSIFIXXJCH-UHFFFAOYSA-N n-(4-hydroxyphenyl)-2-(1,1,3-trioxo-1,2-benzothiazol-2-yl)acetamide Chemical compound C1=CC(O)=CC=C1NC(=O)CN1S(=O)(=O)C2=CC=CC=C2C1=O PUPNJSIFIXXJCH-UHFFFAOYSA-N 0.000 description 1
- AEMBWNDIEFEPTH-UHFFFAOYSA-N n-tert-butyl-n-ethylnitrous amide Chemical compound CCN(N=O)C(C)(C)C AEMBWNDIEFEPTH-UHFFFAOYSA-N 0.000 description 1
- 208000025189 neoplasm of testis Diseases 0.000 description 1
- 230000012223 nuclear import Effects 0.000 description 1
- 238000003199 nucleic acid amplification method Methods 0.000 description 1
- 230000003204 osmotic effect Effects 0.000 description 1
- 201000008968 osteosarcoma Diseases 0.000 description 1
- 229940092253 ovalbumin Drugs 0.000 description 1
- 238000004806 packaging method and process Methods 0.000 description 1
- 201000002528 pancreatic cancer Diseases 0.000 description 1
- 208000008443 pancreatic carcinoma Diseases 0.000 description 1
- 208000004019 papillary adenocarcinoma Diseases 0.000 description 1
- 201000010198 papillary carcinoma Diseases 0.000 description 1
- 244000052769 pathogen Species 0.000 description 1
- 230000001717 pathogenic effect Effects 0.000 description 1
- 108010024744 peptide NY-ESO-1 157-165 Proteins 0.000 description 1
- 239000000813 peptide hormone Substances 0.000 description 1
- 210000003819 peripheral blood mononuclear cell Anatomy 0.000 description 1
- 239000008194 pharmaceutical composition Substances 0.000 description 1
- WVDDGKGOMKODPV-ZQBYOMGUSA-N phenyl(114C)methanol Chemical compound O[14CH2]C1=CC=CC=C1 WVDDGKGOMKODPV-ZQBYOMGUSA-N 0.000 description 1
- 208000024724 pineal body neoplasm Diseases 0.000 description 1
- 201000004123 pineal gland cancer Diseases 0.000 description 1
- 239000013600 plasmid vector Substances 0.000 description 1
- 229920000729 poly(L-lysine) polymer Polymers 0.000 description 1
- 208000037244 polycythemia vera Diseases 0.000 description 1
- 238000002360 preparation method Methods 0.000 description 1
- 125000002924 primary amino group Chemical group [H]N([H])* 0.000 description 1
- 230000008569 process Effects 0.000 description 1
- 230000002062 proliferating effect Effects 0.000 description 1
- 125000001500 prolyl group Chemical group [H]N1C([H])(C(=O)[*])C([H])([H])C([H])([H])C1([H])[H] 0.000 description 1
- 108010014614 prolyl-glycyl-proline Proteins 0.000 description 1
- 108020001580 protein domains Proteins 0.000 description 1
- 230000012743 protein tagging Effects 0.000 description 1
- 230000002797 proteolythic effect Effects 0.000 description 1
- 208000009305 pseudorabies Diseases 0.000 description 1
- 235000008001 rakum palm Nutrition 0.000 description 1
- 238000004064 recycling Methods 0.000 description 1
- 230000001172 regenerating effect Effects 0.000 description 1
- 230000002441 reversible effect Effects 0.000 description 1
- 201000009410 rhabdomyosarcoma Diseases 0.000 description 1
- 102220251380 rs1421690648 Human genes 0.000 description 1
- 239000000523 sample Substances 0.000 description 1
- 238000013515 script Methods 0.000 description 1
- 201000008407 sebaceous adenocarcinoma Diseases 0.000 description 1
- 230000000405 serological effect Effects 0.000 description 1
- 208000000587 small cell lung carcinoma Diseases 0.000 description 1
- 210000000952 spleen Anatomy 0.000 description 1
- 206010041823 squamous cell carcinoma Diseases 0.000 description 1
- 201000011549 stomach cancer Diseases 0.000 description 1
- 208000003265 stomatitis Diseases 0.000 description 1
- 201000010965 sweat gland carcinoma Diseases 0.000 description 1
- 230000001360 synchronised effect Effects 0.000 description 1
- 206010042863 synovial sarcoma Diseases 0.000 description 1
- 230000008685 targeting Effects 0.000 description 1
- 201000003120 testicular cancer Diseases 0.000 description 1
- 230000009258 tissue cross reactivity Effects 0.000 description 1
- 230000009261 transgenic effect Effects 0.000 description 1
- 230000014616 translation Effects 0.000 description 1
- 238000011282 treatment Methods 0.000 description 1
- 210000004881 tumor cell Anatomy 0.000 description 1
- 238000012285 ultrasound imaging Methods 0.000 description 1
- 241001529453 unidentified herpesvirus Species 0.000 description 1
- 208000010570 urinary bladder carcinoma Diseases 0.000 description 1
- 108010094106 vesicular stomatitis virus nucleoprotein (52-59) Proteins 0.000 description 1
- 230000009385 viral infection Effects 0.000 description 1
Classifications
-
- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
- G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
- G01N33/6848—Methods of protein analysis involving mass spectrometry
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K39/0005—Vertebrate antigens
- A61K39/0011—Cancer antigens
- A61K39/001184—Cancer testis antigens, e.g. SSX, BAGE, GAGE or SAGE
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K39/46—Cellular immunotherapy
- A61K39/461—Cellular immunotherapy characterised by the cell type used
- A61K39/4611—T-cells, e.g. tumor infiltrating lymphocytes [TIL], lymphokine-activated killer cells [LAK] or regulatory T cells [Treg]
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K39/46—Cellular immunotherapy
- A61K39/464—Cellular immunotherapy characterised by the antigen targeted or presented
- A61K39/4643—Vertebrate antigens
- A61K39/4644—Cancer antigens
- A61K39/464484—Cancer testis antigens, e.g. SSX, BAGE, GAGE or SAGE
- A61K39/464488—NY-ESO
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P35/00—Antineoplastic agents
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
- C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
- C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
- C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
- C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
- C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
- C07K14/4748—Tumour specific antigens; Tumour rejection antigen precursors [TRAP], e.g. MAGE
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
- C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
- C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
-
- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
-
- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
- G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
- G01N33/6845—Methods of identifying protein-protein interactions in protein mixtures
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
- A61K2039/53—DNA (RNA) vaccination
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/60—Medicinal preparations containing antigens or antibodies characteristics by the carrier linked to the antigen
- A61K2039/6031—Proteins
- A61K2039/6075—Viral proteins
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2319/00—Fusion polypeptide
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N2760/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses negative-sense
- C12N2760/00011—Details
- C12N2760/16011—Orthomyxoviridae
- C12N2760/16111—Influenzavirus A, i.e. influenza A virus
- C12N2760/16122—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N2840/00—Vectors comprising a special translation-regulating system
- C12N2840/20—Vectors comprising a special translation-regulating system translation of more than one cistron
- C12N2840/203—Vectors comprising a special translation-regulating system translation of more than one cistron having an IRES
-
- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N2500/00—Screening for compounds of potential therapeutic value
Landscapes
- Health & Medical Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Chemical & Material Sciences (AREA)
- Engineering & Computer Science (AREA)
- Molecular Biology (AREA)
- Immunology (AREA)
- General Health & Medical Sciences (AREA)
- Medicinal Chemistry (AREA)
- Microbiology (AREA)
- Biomedical Technology (AREA)
- Physics & Mathematics (AREA)
- Organic Chemistry (AREA)
- Biochemistry (AREA)
- Genetics & Genomics (AREA)
- Hematology (AREA)
- Urology & Nephrology (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Veterinary Medicine (AREA)
- Biophysics (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Public Health (AREA)
- Cell Biology (AREA)
- Animal Behavior & Ethology (AREA)
- Pharmacology & Pharmacy (AREA)
- Biotechnology (AREA)
- Mycology (AREA)
- Epidemiology (AREA)
- Zoology (AREA)
- Pathology (AREA)
- Bioinformatics & Computational Biology (AREA)
- Food Science & Technology (AREA)
- Analytical Chemistry (AREA)
- General Physics & Mathematics (AREA)
- Oncology (AREA)
- Toxicology (AREA)
- Gastroenterology & Hepatology (AREA)
- Wood Science & Technology (AREA)
- General Engineering & Computer Science (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
Abstract
The invention disclosed herein is directed to methods of identifying a polypeptide suitable for epitope liberation including, for example, the steps of identifying an epitope of interest; providing a substrate polypeptide sequence including the epitope, wherein the substrate polypeptide permits processing by a proteasome; contacting the substrate polypeptide with a composition including the proteasome, under conditions that support processing of the substrate polypeptide by the proteasome; and assaying for liberation of the epitope. The invention further relates to vectors including a housekeeping epitope expression cassette. The housekeeping epitope(s) can be derived from a target-associated antigen, and the housekeeping epitope can be liberatable, that is capable of liberation, from a translation product of the cassette by immunoproteasome processing. The invention also relates to a method of activating a T cell comprising contacting a substrate polypeptide with an APC
and contacting the APC with a T cell.
and contacting the APC with a T cell.
Description
EXPRESSION VECTORS ENCODING EPITOPES OF
TARGET-ASSOCIATED ANTIGENS AND METHODS FOR THEIR DESIGN
Background of the Invention Field of the Invention S [0001] The invention disclosed herein is directed to methods for the design of epitope-encoding vectors for use in compositions, including for example, pharmaceutical compositions capable of inducing an immune response in a subject to whom the compositions are administered.
The invention is further directed to the vectors themselves. The epitope(s) expressed using such vectors can stimulate a cellular immune response against a target cell displaying the epitope(s).
Description of the Related Art [0002] The immune system can be categorized into two discrete effector arms.
The first is innate immunity, which involves numerous cellular components and soluble factors that respond to all infectious challenges. The other is the adaptive immune response, which is customized to respond specifically to precise epitopes from infectious agents.
The adaptive immune response is further broken down into two effector arms known as the humoral and cellular immune systems. The humoral arm is centered on the production of antibodies by B-lymphocytes while the cellular arm involves the killer cell activity of cytotoxic T
Lymphocytes.
TARGET-ASSOCIATED ANTIGENS AND METHODS FOR THEIR DESIGN
Background of the Invention Field of the Invention S [0001] The invention disclosed herein is directed to methods for the design of epitope-encoding vectors for use in compositions, including for example, pharmaceutical compositions capable of inducing an immune response in a subject to whom the compositions are administered.
The invention is further directed to the vectors themselves. The epitope(s) expressed using such vectors can stimulate a cellular immune response against a target cell displaying the epitope(s).
Description of the Related Art [0002] The immune system can be categorized into two discrete effector arms.
The first is innate immunity, which involves numerous cellular components and soluble factors that respond to all infectious challenges. The other is the adaptive immune response, which is customized to respond specifically to precise epitopes from infectious agents.
The adaptive immune response is further broken down into two effector arms known as the humoral and cellular immune systems. The humoral arm is centered on the production of antibodies by B-lymphocytes while the cellular arm involves the killer cell activity of cytotoxic T
Lymphocytes.
[0003] Cytotoxic T Lymphocytes (CTL) do not recognize epitopes on the infectious agents themselves. Rather, CTL detect fragments of antigens derived from infectious agents that are displayed on the surface of infected cells. As a result antigens are visible to CTL only after they have been processed by the infected cell and thus displayed on the surface of the cell.
[0004] The antigen processing and display system on the surface of cells has been well established. CTL recognize short peptide antigens, which are displayed on the surface in non-covalent association with class I major histocompatibility complex molecules (MHC). These class I peptides are in turn derived from the degradation of cytosolic proteins.
Summary of the Invention [0005] Embodiments of the invention provide expression cassettes, for example, for use in vaccine vectors, which encode one or more embedded housekeeping epitopes, and methods for designing and testing such expression cassettes. Housekeeping epitopes can be liberated from the translation product of such cassettes through proteolytic processing by the immunoproteasome of professional antigen presenting cells (pAPC). In one embodiment of the invention, sequences flanking the housekeeping epitope(s) can be altered to promote cleavage by the immunoproteasome at the desired location(s). Housekeeping epitopes, their uses, and identification are described in U.S. Patent Application Nos. 09/560,465 and 09/561,074 entitled EPITOPE
SYNCHRONIZATION IN ANTIGEN PRESENTING CELLS, and METHOD OF EPITOPE
DISCOVERY, respectively; both of which were filed on April 28, 2000.
Summary of the Invention [0005] Embodiments of the invention provide expression cassettes, for example, for use in vaccine vectors, which encode one or more embedded housekeeping epitopes, and methods for designing and testing such expression cassettes. Housekeeping epitopes can be liberated from the translation product of such cassettes through proteolytic processing by the immunoproteasome of professional antigen presenting cells (pAPC). In one embodiment of the invention, sequences flanking the housekeeping epitope(s) can be altered to promote cleavage by the immunoproteasome at the desired location(s). Housekeeping epitopes, their uses, and identification are described in U.S. Patent Application Nos. 09/560,465 and 09/561,074 entitled EPITOPE
SYNCHRONIZATION IN ANTIGEN PRESENTING CELLS, and METHOD OF EPITOPE
DISCOVERY, respectively; both of which were filed on April 28, 2000.
[0006] Examples of housekeeping epitopes are disclosed in provisional U.S.
Patent Applications entitled EPITOPE SEQUENCES, Nos. 60/282,211, filed on April 6, 2001;
60/337,017, filed on November 7, 2001; 60/363210 filed 3/7/02; and 60/409,123, filed on September 5, 2002; and U.S. Application No. 10/117,937, filed on April 4, 2002, which is also entitled EPITOPE SEQUENCES.
Patent Applications entitled EPITOPE SEQUENCES, Nos. 60/282,211, filed on April 6, 2001;
60/337,017, filed on November 7, 2001; 60/363210 filed 3/7/02; and 60/409,123, filed on September 5, 2002; and U.S. Application No. 10/117,937, filed on April 4, 2002, which is also entitled EPITOPE SEQUENCES.
[0007] In other embodiments of the invention, the housekeeping epitope(s) can be flanked by arbitrary sequences or by sequences incorporating residues known to be favored in immunoproteasome cleavage sites. As used herein the term "arbitrary sequences"
refers to sequences chosen without reference to the native sequence context of the epitope, their ability to promote processing, or immunological function. In further embodiments of the invention multiple epitopes can be arrayed head-to-tail. These arrays can be made up entirely of housekeeping epitopes. Likewise, the arrays can include alternating housekeeping and immune epitopes.
Alternatively, the arrays can include housekeeping epitopes flanked by immune epitopes, whether complete or distally truncated. Further, the arrays can be of any other similar arrangement. There is no restriction on placing a housekeeping epitope at the terminal positions of the array. The vectors can additionally contain authentic protein coding sequences or segments thereof containing epitope clusters as a source of immune epitopes. The term "authentic" refers to natural protein sequences.
refers to sequences chosen without reference to the native sequence context of the epitope, their ability to promote processing, or immunological function. In further embodiments of the invention multiple epitopes can be arrayed head-to-tail. These arrays can be made up entirely of housekeeping epitopes. Likewise, the arrays can include alternating housekeeping and immune epitopes.
Alternatively, the arrays can include housekeeping epitopes flanked by immune epitopes, whether complete or distally truncated. Further, the arrays can be of any other similar arrangement. There is no restriction on placing a housekeeping epitope at the terminal positions of the array. The vectors can additionally contain authentic protein coding sequences or segments thereof containing epitope clusters as a source of immune epitopes. The term "authentic" refers to natural protein sequences.
[0008] Epitope clusters and their uses are described in U.S. Patent application Nos.
09/561,571 entitled EPITOPE CLUSTERS, filed on April 28, 2000; 10/005,905, entitled EPITOPE
SYNCHRONIZATION IN ANTIGEN PRESENTING CELLS, filed on November 7, 2001; and 10/026,066, filed on December 7, 2001, also entitled EPITOPE SYNCHRONIZATION
IN
ANTIGEN PRESENTING CELLS.
09/561,571 entitled EPITOPE CLUSTERS, filed on April 28, 2000; 10/005,905, entitled EPITOPE
SYNCHRONIZATION IN ANTIGEN PRESENTING CELLS, filed on November 7, 2001; and 10/026,066, filed on December 7, 2001, also entitled EPITOPE SYNCHRONIZATION
IN
ANTIGEN PRESENTING CELLS.
[0009] Embodiments of the invention can encompass screening the constructs to determine whether the housekeeping epitope is liberated. In constructs containing multiple housekeeping epitopes, embodiments can include screening to determine which epitopes are liberated. In a preferred embodiment, a vector containing an embedded epitope can be used to immunize HLA transgenic mice and the resultant CTL can be tested for their ability to recognize target cells presenting the mature epitope. In another embodiment, target cells expressing immunoproteasome can be transformed with the vector. The target cell may express immunoproteasome either constitutively, because of treatment with interferon (IFN), or through genetic manipulation, for example. CTL that recognize the mature epitope can be tested for their ability to recognize these target cells. In yet another embodiment, the embedded epitope can be prepared as a synthetic peptide. The synthetic peptide then can be subjected to digestion by an immunoproteasome preparation in vitro and the resultant fragments can be analyzed to determine the sites of cleavage. Such polypeptides, recombinant or synthetic, from which embedded epitopes can be successfully liberated, can also be incorporated into immunogenic compositions.
[0010] The invention disclosed herein relates to the identification of a polypeptide suitable for epitope liberation. One embodiment of the invention, relates to a method of identifying a polypeptide suitable for epitope liberation including, for example, the steps of identifying an epitope of interest; providing a substrate polypeptide sequence including the epitope, wherein the substrate polypeptide permits processing by a proteasome; contacting the substrate polypeptide with a composition including the proteasome, under conditions that support processing of the substrate polypeptide by the proteasome; and assaying for liberation of the epitope.
[0011] The epitope can be embedded in the substrate polypeptide, and in some aspects the substrate polypeptide can include more than one epitope, for example.
Also, the epitope can be a housekeeping epitope.
Also, the epitope can be a housekeeping epitope.
[0012] In one aspect, the substrate polypeptide can be a synthetic peptide.
Optionally, the substrate polypeptide can be included in a formulation promoting protein transfer.
Alternatively, the substrate polypeptide can be a fusion protein. The fusion protein can further include a protein domain possessing protein transfer activity. Further, the contacting step can include immunization with the substrate polypeptide.
Optionally, the substrate polypeptide can be included in a formulation promoting protein transfer.
Alternatively, the substrate polypeptide can be a fusion protein. The fusion protein can further include a protein domain possessing protein transfer activity. Further, the contacting step can include immunization with the substrate polypeptide.
[0013] In another aspect, the substrate polypeptide can be encoded by a polynucleotide. The contacting step can include immunization with a vector including the polynucleotide, for example. The immunization can be carried out in an HLA-transgenic mouse or any other suitable animal, for example. Alternatively, the contacting step can include transforming a cell with a vector including the polynucleotide. In some embodiments the transformed cell can be a target cell that is targeted by CTL for purposes of assaying for proper liberation of epitope.
[0014] The proteasome processing can take place intracellularly, either in vitro or in vivo. Further, the proteasome processing can take place in a cell-free system.
[0015] The assaying step can include a technique selected from the group including, but not limited to, mass spectrometry, N-terminal pool sequencing, HPLC, and the like. Also, the assaying step can include a T cell target recognition assay. The T cell target recognition assay can be selected from the group including, but not limited to, a cytolytic activity assay, a chromium release assay, a cytokine assay, an ELISPOT assay, tetramer analysis, and the like.
[0016] In still another aspect, the amino acid sequence of the substrate polypeptide including the epitope can be arbitrary. Also, the substrate polypeptide in which the epitope is embedded can be derived from an authentic sequence of a target-associated antigen. Further, the substrate polypeptide in which the epitope is embedded can be conformed to a preferred immune proteasome cleavage site flanking sequence.
[0017] In another aspect, the substrate polypeptide can include an array of additional epitopes. Members of the array can be arranged head-to-tail, for example. The array can include more than one housekeeping epitope. The more than one housekeeping epitope can include copies of the same epitope. The array can include a housekeeping and an immune epitope, or alternating housekeeping and immune epitopes, for example. Also, the array can include a housekeeping epitope positioned between two immune epitopes in an epitope battery. The array can include multiple epitope batteries, so that there are two immune epitopes between each housekeeping epitope in the interior of the array. Optionally, at least one of the epitopes can be truncated distally to its junction with an adjacent epitope. The truncated epitopes can be immune epitopes, for example. The truncated epitopes can have lengths selected from the group including, but not limited to, 9, 8, 7, 6, 5, 4 amino acids, and the like.
[0018) In still another aspect, the substrate polypeptide can include an array of epitopes and epitope clusters. Members of the array can be arranged head-to-tail, for example.
[0019] In yet another aspect, the proteasome can be an immune proteasome.
1 S [0020] Another embodiment of the disclosed invention relates to vectors including a housekeeping epitope expression cassette. The housekeeping epitope(s) can be derived from a target-associated antigen, and the housekeeping epitope can be liberatable, that is capable of liberation, from a translation product of the cassette by immunoproteasome processing.
[0021] In one aspect of the invention the expression cassette can encode an array of two or more epitopes or at least one epitope and at least one epitope cluster.
The members of the array can be arranged head-to-tail, for example. Also, the members of the array can be arranged head-to-tail separated by spacing sequences, for example. Further, the array can include a plurality of housekeeping epitopes. The plurality of housekeeping epitopes can include more than one copy of the same epitope or single copies of distinct epitopes, for example. The array can include at least one housekeeping epitope and at least one immune epitope. Also, the array can include alternating housekeeping and immune epitopes. Further, the array includes a housekeeping epitope sandwiched between two immune epitopes so that there are two immune epitopes between each housekeeping epitope in the interior of the array. The immune epitopes can be truncated distally to their junction with the adjacent housekeeping epitope.
[0022] In another aspect, the expression cassette further encodes an authentic protein sequence, or segment thereof, including at least one immune epitope.
Optionally, the segment can include at least one epitope cluster. The housekeeping epitope expression cassette and the authentic sequence including at least one immune epitope can be encoded in a single reading frame or transcribed as a single mRNA species, for example. Also, the housekeeping epitope expression cassette and the authentic sequence including at least one immune epitope may not be transcribed as a single mRNA species.
[0023) In yet another aspect, the vector can include a DNA molecule or an RNA
molecule. The vector can encode, for example, SEQ )D NO. 4, SEQ 117 NO. 17, SEQ )D NO. 20, SEQ ID NO. 26, SEQ Il7'NO. 27, SEQ ID NO. 29, SEQ ID NO. 33, and the like.
Also, the vector can include SEQ >I7 NO. 9, SEQ ID NO. 19, SEQ >D NO. 21, SEQ ID NO. 30, SEQ ID
NO. 34, and the like. Also, the vector can encode SEQ ID NO. 5 or SEQ I17 NO. 18, for example.
[0024] In still another aspect, the target-associated antigen can be an antigen derived from or associated with a tumor or an intracellular parasite, and the intracellular parasite can be, for example, a virus, a bacterium, a protozoan, or the like.
[0025] Another embodiment of the invention relates to vectors including a housekeeping epitope identified according to any of the methods disclosed herein, claimed or otherwise. For example, embodiments can relate to vector encoding a substrate polypeptide that includes a housekeeping epitope by any of the methods described herein.
[0026) In one aspect, the housekeeping epitope can be liberated from the cassette translation product by immune proteasome processing [0027] Another embodiment of the disclosed invention relates to methods of activating a T cell. The methods can include, for example, the steps of contacting a vector including a housekeeping epitope expression cassette with an APC. The housekeeping epitope can be derived from a target-associated antigen, for example, and the housekeeping epitope can be liberatable from a translation product of the cassette by immunoproteasome processing. The methods can further include contacting the APC with a T cell. The contacting of the vector with the APC can occur in vitro or in vivo.
[0028] Another embodiment of the disclosed invention relates to a substrate polypeptide including a housekeeping epitope wherein the housekeeping epitope can be liberated by immunoproteasome processing in a pAPC.
[0029] Another embodiment of the disclosed invention relates to a method of activating a T cell comprising contacting a substrate polypeptide including a housekeeping epitope with an APC wherein the housekeeping epitope can be liberated by immunoproteasome processing and contacting the APC with a T cell.
Brief Description of the Drawings [0030] Figure 1. An illustrative drawing depicting pMA2M.
[0031] Figure 2. Assay results showing the % of specific lysis of ELAGIGII,TV
pulsed and unpulsed T2 target cells by mock immunized CTL.
[0032) Figure 3. Assay results showing the % of specific lysis of ELAGIGILTV
pulsed and unpulsed T2 target cells by pVAXM3 immunized CTL.
[0033] Figure 4. Assay results showing the % of specific lysis of ELAGIGIL,TV
pulsed and unpulsed T2 target cells by pVAXM2 immunized CTL.
[0034] Figure S. Assay results showing the % of specific lysis of ELAGIGILTV
pulsed and unpulsed T2 target cells by pVAXMl immunized CTL.
[0035] Figure 6. Illustrates a sequence of SEQ m NO. 22 from which the NY-ESO-1 is~abs epitope is liberated by immunoproteasomal processing.
[0036] Figure 7. Shows the differential processing by immunoproteasome and housekeeping proteasome of the SLLMWITQC epitope (SEQ ID NO. 12) in its native context where the cleavage following the C is more efficiently produced by housekeeping than immunoproteasome.
[0037] Figure 8. 8A: Shows the results of the human immunoproteasome digest of SEQ 117 NO. 31. 8B: Shows the comparative results of mouse versus human immunoproteasome digestion of SEQ ID NO. 31.
[0038] Figure 9. Shows the differential processing of SSX-23,_68 by housekeeping and immunoproteasome.
Detailed Description of the Preferred Embodiment Definitions [0039] Unless otherwise clear from the context of the use of a term herein, the following listed terms shall generally have the indicated meanings for purposes of this description.
[0040] PROFESSIONAL ANTIGEN-PRESENTING CELL (pAPC) - a cell that possesses T cell costimulatory molecules and is able to induce a T cell response. Well characterized pAPCs include dendritic cells, B cells, and macrophages.
[0041] PERIPHERAL CELL - a cell that is not a pAPC.
[0042] HOUSEKEEPING PROTEASOME - a proteasome normally active in peripheral cells, and generally not present or not strongly active in pAPCs.
[0043] IMMUNOPROTEASOME - a proteasome normally active in pAPCs; the immunoproteasome is also active in some peripheral cells in infected tissues or following exposure to interferon.
[0044] EPITOPE - a molecule or substance capable of stimulating an immune response. In preferred embodiments, epitopes according to this definition include but are not necessarily limited to a polypeptide and a nucleic acid encoding a polypeptide, wherein the polypeptide is capable of stimulating an immune response. In other preferred embodiments, epitopes according to this definition include but are not necessarily limited to peptides presented on the surface of cells, the peptides being non-covalently bound to the binding cleft of class I MHC, such that they can interact with T cell receptors (TCR). Epitopes presented by class I MHC may be in immature or mature form. "Mature" refers to an MHC epitope in distinction to any precursor ("immature") that may include or consist essentially of a housekeeping epitope, but also includes other sequences in a primary translation product that are removed by processing, including without limitation, alone or in any combination, proteasomal digestion, N-terminal trimming, or the action of exogenous enzymatic activities. Thus, a mature epitope may be provided embedded in a somewhat longer polypeptide, the immunological potential of which is due, at least in part, to the embedded epitope; or in its ultimate form that can bind in the MHC binding cleft to be recognized by TCR, respectively.
[0045] MHC EPITOPE - a polypeptide having a known or predicted binding affinity for a mammalian class I or class II major histocompatibility complex (MHC) molecule.
[0046] HOUSEKEEPING EPITOPE - In a preferred embodiment, a housekeeping epitope is defined as a polypeptide fragment that is an MHC epitope, and that is displayed on a cell in which housekeeping proteasomes are predominantly active. In another preferred embodiment, a housekeeping epitope is defined as a polypeptide containing a housekeeping epitope according to the foregoing definition, that is flanked by one to several additional amino acids. In another preferred embodiment, a housekeeping epitope is defined as a nucleic acid that encodes a housekeeping epitope according to the foregoing definitions. Exemplary housekeeping epitopes are provide in U.S. Application No. 10/117,937, filed on April 4, 2002; and U.S. Provisional Application Nos. 60/282,211, filed on April 6, 2001; 60/337,017, filed on November 7, 2001;
60/363210 filed 3/7/02; and 60/409,123, filed on September 5, 2002; all of which are entitled EPITOPE SEQUENCES.
[0047) IMMUNE EPITOPE - In a preferred embodiment, an immune epitope is defined as a polypeptide fragment that is an MHC epitope, and that is displayed on a cell in which immunoproteasomes are predominantly active. In another preferred embodiment, an immune epitope is defined as a polypeptide containing an immune epitope according to the foregoing definition, that is flanked by one to several additional amino acids. In another preferred embodiment, an immune epitope is defined as a polypeptide including an epitope cluster sequence, having at least two polypeptide sequences having a known or predicted affinity for a class I MHC.
In yet another preferred embodiment, an immune epitope is defined as a nucleic acid that encodes an immune epitope according to any of the foregoing definitions.
[0048] TARGET CELL - a cell to be targeted by the vaccines and methods of the invention. Examples of target cells according to this definition include but are not necessarily limited to: a neoplastic cell and a cell harboring an intracellular parasite, such as, for example, a virus, a bacterium, or a protozoan. Target cells can also include cells that are targeted by CTL as a part of assays to determine or confirm proper epitope liberation and processing by a cell expressing immunoproteasome, to determine T cell specificity or immunogenicity for a desired epitope.. Such cells may be transfored to express the substrate or liberation sequence, or the cells can simply be pulsed with peptidelepitope.
[0049] TARGET-ASSOCIATED ANTIGEN (TAA) - a protein or polypeptide present in a target cell.
[0050] TUMOR-ASSOCIATED ANTIGENS (TuAA) - a TAA, wherein the target cell is a neoplastic cell.
[0051) HLA EPITOPE - a polypeptide having a known or predicted binding affinity for a human class I or class II HLA complex molecule.
[0052] ANTIBODY - a natural immunoglobulin (Ig), poly- or monoclonal, or any molecule composed in whole or in part of an Ig binding domain, whether derived biochemically or by use of recombinant DNA. Examples include inter alia, F(ab), single chain Fv, and Ig variable region-phage coat protein fusions.
[0053] ENCODE - an open-ended term such that a nucleic acid encoding a particular amino acid sequence can consist of codons specifying that (poly)peptide, but can also comprise additional sequences either translatable, or for the control of transcription, translation, or replication, or to facilitate manipulation of some host nucleic acid construct.
[0054] SUBSTANTIAL SIMILARITY - this term is used to refer to sequences that differ from a reference sequence in an inconsequential way as judged by examination of the sequence. Nucleic acid sequences encoding the same amino acid sequence are substantially similar despite differences in degenerate positions or modest differences in length or composition of any non-coding regions. Amino acid sequences differing only by conservative substitution or minor length variations are substantially similar. Additionally, amino acid sequences comprising housekeeping epitopes that differ in the number of N-terminal flanking residues, or immune epitopes and epitope clusters that differ in the number of flanking residues at either terminus, are substantially similar. Nucleic acids that encode substantially similar amino acid sequences are themselves also substantially similar.
[0055] FUNCTIONAL SIMILARITY - this term is used to refer to sequences that differ from a reference sequence in an inconsequential way as judged by examination of a biological or biochemical property, although the sequences may not be substantially similar. For example, two nucleic acids can be useful as hybridization probes for the same sequence but encode differing amino acid sequences. Two peptides that induce cross-reactive CTL
responses are functionally similar even if they differ by non-conservative amino acid substitutions (and thus do not meet the substantial similarity definition). Pairs of antibodies, or TCRs, that recognize the same epitope can be functionally similar to each other despite whatever structural differences exist.
In testing for functional similarity of immunogenicity one would generally immunize with the "altered" antigen and test the ability of the elicited response (Ab, CTL, cytokine production, etc.) 3 5 to recognize the target antigen. Accordingly, two sequences may be designed to differ in certain _g_ respects while retaining the same function. Such designed sequence variants are among the embodiments of the present invention.
[0056] EXPRESSION CASSETTE - a polynucleotide sequence encoding a polypeptide, operably linked to a promoter and other transcription and translation control elements, including but not limited to enhancers, termination codons, internal ribosome entry sites, and polyadenylation sites. The cassette can also include sequences that facilitate moving it from one host molecule to another.
[0057) EMBEDDED EPITOPE - an epitope contained within a longer polypeptide, also can include an epitope in which either the N- terminus or the C-terminus is embedded such that the epitope is not in an interior position.
[0058] MATURE EPITOPE - a peptide with no additional sequence beyond that present when the epitope is bound in the MHC peptide-binding cleft.
[0059] EPITOPE CLUSTER - a polypeptide, or a nucleic acid sequence encoding it, that is a segment of a native protein sequence comprising two or more known or predicted epitopes with binding affinity for a shared MHC restriction element, wherein the density of epitopes within the cluster is greater than the density of all known or predicted epitopes with binding affinity for the shared MHC restriction element within the complete protein sequence, and as disclosed in U.S.
Patent Application No. 09/561,571 entitled EPITOPE CLUSTERS.
[0060] Substrate or liberation sequence- a designed or engineered sequence comprising or encoding a housekeeping epitope (according to the first of the definitions offered above) embedded in a larger sequence that provides a context allowing the housekeeping epitope to be liberated by immunoproteasomal processing, directly or in combination with N-terminal trimming or other processes.
[0061) Degradation of cytosolic proteins takes place via the ubiquitin-dependent multi-catalytic multi-subunit protease system known as the proteasome. The proteasome degrades cytosolic proteins generating fragments that can then be translocated from the cytosol into the endoplasmic reticulum (ER) for loading onto class I MHC. Such protein fragments shall be referred to as class I peptides. The peptide loaded MHC are subsequently transported to the cell surface where they can be detected by CTL.
[0062] The mufti-catalytic activity of the proteasome is the result of its mufti-subunit structure. Subunits are expressed from different genes and assembled post-translationally into the proteasome complex. A key feature of the proteasome is its bimodal activity, which enables it to exert its protease, or cleavage function, with two discrete kinds of cleavage patterns. This bimodal action of the proteasome is extremely fundamental to understanding how CTL are targeted to recognize peripheral cells in the body and how this targeting requires synchronization between the immune system and the targeted cells.
[0063] The housekeeping proteasome is constitutively active in all peripheral cells and tissues of the body. The first mode of operation for the housekeeping proteasome is to degrade cellular protein, recycling it into amino acids. Proteasome function is therefore a necessary activity for cell life. As a corollary to its housekeeping protease activity, however, class I peptides generated by the housekeeping proteasome are presented on all of the peripheral cells of the body.
[0064] The proteasome's second mode of function is highly exclusive and occurs specifically in pAPCs or as a consequence of a cellular response to interferons (IFNs). In its second mode of activity the proteasome incorporates unique subunits, which replace the catalytic subunits of the constitutive housekeeping proteasome. This "modified"
proteasome has been called the immunoproteasome, owing to its expression in pAPC and as a consequence of induction by IFN
in body cells.
[0065] APC define the repertoire of CTL that recirculate through the body and are potentially active as killer cells. CTL are activated by interacting with class I peptide presented on the surface of a pAPC. Activated CTL are induced to proliferate and caused to recirculate through the body in search of diseased cells. This is why the CTL response in the body is defined specifically by the class I peptides produced by the pAPC. It is important to remember that pAPCs express the immunoproteasome, and that as a consequence of the bimodal activity of the proteasome, the cleavage pattern of proteins (and the resultant class I
peptides produced) are different from those in peripheral body cells which express housekeeping proteasome. The differential proteasome activity in pAPC and peripheral body cells, therefore, is important to consider during natural infection and with therapeutic CTL vaccination strategies.
[0066] All cells of the body are capable of producing IFN in the event that they are infected by a pathogen such as a virus. IFN production in turn results in the expression of the immunoproteasome in the infected cell. Viral antigens are thereby processed by the immunoproteasome of the infected cell and the consequent peptides are displayed with class I
MHC on the cell surface. At the same time, pAPC are sequestering virus antigens and are processing class I peptides with their immunoproteasome activity, which is normal for the pAPC
cell type. The CTL response in the body is being stimulated specifically by the class I peptides produced by the pAPC. Fortunately, the infected cell is also producing class I
peptides from the immunoproteasome, rather than the normal housekeeping proteasome. Thus, virus-related class I
peptides are being produced that enable detection by the ensuing CTL response.
The CTL immune response is induced by pAPC, which normally produce different class I peptides compared to peripheral body cells, owing to different proteasome activity. Therefore, during infection there is epitope synchronization between the infected cell and the immune system.
[0067] This is not the case with tumors and chronic viruses, which block the interferon system. For tumors there is no infection in the tumor cell to induce the immunoproteasome expression, and chronic virus infection either directly or indirectly blocks immunoproteasome expression. In both cases the diseased cell maintains its display of class I
peptides derived from housekeeping proteasome activity and avoids effective surveillance by CTL.
[0068) In the case of therapeutic vaccination to eradicate tumors or chronic infections, the bimodal function of the proteasome and its differential activity in APC
and peripheral cells of the body is significant. Upon vaccination with protein antigen, and before a CTL response can occur, the antigen must be acquired and processed into peptides that are subsequently presented on class I MHC on the pAPC surface. The activated CTL recirculate in search of cells with similar class I peptide on the surface. Cells with this peptide will be subjected to destruction by the cytolytic activity of the CTL. If the targeted diseased cell does not express the immunoproteasome, which is present in the pAPC, then the epitopes are not synchronized and CTL
fail to find the desired peptide target on the surface of the diseased cell.
[0069] Preferably, therapeutic vaccine design takes into account the class I
peptide that is actually present on the target tissue. That is, effective antigens used to stimulate CTL to 1 S attack diseased tissue are those that are naturally processed and presented on the surface of the diseased tissue. For tumors and chronic infection this generally means that the CTL epitopes are those that have been processed by the housekeeping proteasome. Tn order to generate an effective therapeutic vaccine, CTL epitopes are identified based on the knowledge that such epitopes are, in fact, produced by the housekeeping proteasome system. Once identified, these epitopes, embodied as peptides, can be used to successfully immunize or induce therapeutic CTL
responses against housekeeping proteasome expressing target cells in the host.
[0070] However, in the case of DNA vaccines, there can be an additional consideration. The immunization with DNA requires that APCs take up the DNA
and express the encoded proteins or peptides. It is possible to encode a discrete class I
peptide on the DNA. By immunizing with this construct, APCs can be caused to express a housekeeping epitope, which is then displayed on class I MHC on the surface of the cell for stimulating an appropriate CTL
response. Constructs for generation of proper termini of housekeeping epitopes have been described in U.S. Patent application No. 09/561,572 entitled EXPRESSION
VECTORS
ENCODING EPITOPES OF TARGET-ASSOCIATED ANTIGENS, filed on April 28, 2000.
[0071) Embodiments of the invention provide expression cassettes that encode one or more embedded housekeeping epitopes, and methods far designing and testing such expression cassettes. The expression cassettes and constructs can encode epitopes, including housekeeping epitopes, derived from antigens that are associated with targets. Housekeeping epitopes can be liberated from the translation products) of the cassettes. For example, in some embodiments of 3 5 the invention, the housekeeping epitope(s) can be flanked by arbitrary sequences or by sequences incorporating residues known to be favored in immunoproteasome cleavage sites.
In further embodiments of the invention multiple epitopes can be arrayed head-to-tail. In some embodiments, these arrays can be made up entirely of housekeeping epitopes. Likewise, the arrays can include alternating housekeeping and immune epitopes. Alternatively, the arrays can include housekeeping epitopes flanked by immune epitopes, whether complete or distally truncated.
In some preferred embodiments, each housekeeping epitope can be flanked on either side by an immune epitope, such that an array of such arrangements has two immune epitopes between each housekeeping epitope.
Further, the arrays can be of any other similar arrangement. There is no restriction on placing a housekeeping epitope at the terminal positions of the array. The vectors can additionally contain authentic protein coding sequences or segments thereof containing epitope clusters as a source of immune epitopes.
[0072] Several disclosures make reference to polyepitopes or string-of bead arrays.
See, for example, W00119408A1, March 22, 2001; W09955730A2, November 4, 1999;
W00040261A2, July 13, 2000; W09603144A1, February 8, 1996; EP1181314A1, February 27, 2002; W00123577A3, April 5; US6074817, June 13, 2000; US5965381, October 12, 1999;
W09741440A1, November 6, 1997; US6130066, October 10, 2000; US6004777, December 21, 1999; US5990091, November 23, 1999; W09840501A1, September 17, 1998;
W09840500A1, September 17, 1998; W00118035A2, March 15, 2001; W002068654A2, September 6, 2002;
W00189281A2, November 29, 2001; W00158478A, August 16, 2001; EP1118860A1, July 25, 2001; W00111040A1, February 15, 2001; W00073438A1, December 7, 2000;
W00071158A1, November 30, 2000; W00066727A1, November 9, 2000; W00052451A1, September 8, 2000;
W00052157A1, September 8, 2000; W00029008A2, May 25, 2000; W00006723A1, February 10, 2000. Additional disclosures, include Palmowski MJ, et al - J Immunol 2002;168(9):4391-8; Fang ZY, et al - Virology 2001;291(2):272-84; Firat H, et al - J Gene Med 2002;4(1):38-45; Smith SG, et al - Clin Cancer Res 2001;7(12):4253-61; Vonderheide RH, et al - Clin Cancer Res 2001;
7(11):3343-8; Firat H, et al - Eur 3 Iznmunol 2001;31(10):3064-74; Le T'T, et al - Vaccine 2001;19(32):4669-75; Fayolle C, et al - J Virol 2001;75(16):7330-8; Smith SG -Curr Opin Mol Ther 1999;1(1):10-5; Firat H, et al - Eur J Immunol 1999;29(10):3112-21; Mateo L, et al - 3 Immunol 1999;163(7):4058-63; Heemskerk MH, et al - Cell Immunol 1999;195(1):10-7;
Woodberry T, et al - J Virol 1999;73(7):5320-S; Hanke T, et al - Vaccine 1998;16(4):426-35;
Thomson SA, et al - J Immunol 1998;160(4):1717-23; Toes RE, et al - Proc Natl Acad Sci USA
1997;94(26):14660-5; Thomson SA, et al - J Immunol 1996;157(2):822-6; Thomson SA, et al -Proc Natl Acad Sci USA 1995;92(13):5845-9; Street MD, et al - Immunology 2002;106(4):526-36;
Hirano K, et al - Histochem Cell Biol 2002;117(1):41-53; Ward SM, et al -Virus Genes 2001;23(1):97-104; Liu WJ, et al - Virology 2000;273(2):374-82; Gariglio P, et al - Arch Med Res 1998;29(4):279-84; Suhrbier A - Immunol Cell Biol 1997;75(4):402-8; Fomsgaard A, et al -Vaccine 1999;18(7-8):681-91; An LL, et al - J Virol 1997;71(3):2292-302;
Whitton JL, et al - J
Virol 1993;67(1):348-52; Ripalti A, et al - J Clin Microbiol 1994;32(2):358-63; and Gilbert, S.C., et al., Nat. Biotech. 15:1280-1284, 1997.
[0073] One important feature that the disclosures in the preceding paragraph all share is their lack of appreciation for the desirability of regenerating housekeeping epitopes when the construct is expressed in a pAPC. This understanding was not apparent until the present invention.
Embodiments of the invention include sequences, that when processed by an immune proteasome, liberate or generate a housekeeping epitope. Embodiments of the invention also can liberate or generate such epitopes in immunogenically effective amounts. Accordingly, while the preceding references contain disclosures relating to polyepitope arrays, none is enabling of the technology necessary to provide or select a polyepitope capable of liberating a housekeeping epitope by action of an immunoproteasome in a pAPC. In contrast, embodiments of the instant invention are based upon a recognition of the desirability of achieving this result. Accordingly, embodiments of the instant invention include any nucleic acid construct that encodes a polypeptide containing at least one housekeeping epitope provided in a context that promotes its generation via immunoproteasomal activity, whether the housekeeping epitope is embedded in a string-of beads array or some other arrangement. Some embodiments of the invention include uses of one or more of the nucleic acid constructs or their products that are specifically disclosed in any one or more of the above-listed references. Such uses include, for example, screening a polyepitope for proper liberation context of a housekeeping epitope and/or an immune epitope, designing an effective immunogen capable of causing presentation of a housekeeping epitope and/or an immune epitope on a pAPC, immunizing a patient, and the like. Alternative embodiments include use of only a subset of such nucleic acid constructs or a single such construct, while specifically excluding one or more other such constructs, for any of the purposes disclosed herein. Some preferred embodiments employ these and/or other nucleic acid sequences encoding polyepitope arrays alone or in combination. For example, some embodiments exclude use of polyepitope arrays from one or more of the above-mentioned references. Other embodiments may exclude any combination or all of the polyepitope arrays from the above-mentioned references collectively.
Some embodiments include viral and/or bacterial vectors encoding polyepitope arrays, while other embodiments specifically exclude such vectors. Such vectors can encode carrier proteins that may have some immunostimulatory effect. Some embodiments include such vectors with such immunostimulatory/immunopotentiating effects, as opposed to immunogenic effects, while in other embodiments such vectors may be included. Further, in some instances viral and bacterial vectors encode the desired epitope as a part of substantially complete proteins which are not associated with the target cell. Such vectors and products are included in some embodiments, while excluded from others. Some embodiments relate to repeated administration of vectors. In some of those embodiments, nonviral and nonbacterial vectors are included. Likewise, some embodiments include arrays that contain extra amino acids between epitopes, for example anywhere from 1-6 amino acids, or more, in some embodiments, while other embodiments specifically exclude such arrays.
[0074) Embodiments of the present invention also include methods, uses, therapies, and compositions directed to various types of targets. Such targets can include, for example, neoplastic cells such as those listed below, for example; and cells infected with any virus, bacterium, protozoan, fungus, or other agents, examples of which are listed below, in Tables 1-5, or which are disclosed in any of the references listed above. Alternative embodiments include the use of only a subset of such neoplastic cells and infected cells listed below, in Tables 1-5, or in any of the references disclosed herein, or a single one of the neoplastic cells or infected cells, while specifically excluding one or more other such neoplastic cells or infected cells, for any of the purposes disclosed herein. The following are examples of neoplastic cells that can be targeted:
human sarcomas and carcinomas, e.g., fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilms' tumor, cervical cancer, testicular tumor, lung carcinoma, small cell lung carcinoma, bladder carcinoma, epithelial carcinoma, glioma, astrocytoma, medulloblastoma, craniopharyngioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, meningioma, melanoma, neuroblastoma, retinoblastoma; leukemias, e.g., acute lymphocytic leukemia and acute myelocytic leukemia (myeloblastic, promyelocytic, myelomonocytic, monocytic and erythroleukemia);
chronic leukemia (chronic myelocytic (granulocytic) leukemia and chronic lymphocytic leukemia);
and polycythemia vera, lymphoma (Hodgkin's disease and non Hodgkin's disease), multiple myeloma, Waldenstrom's macroglobulinemia, heavy chain disease, hepatocellular cancer, brain cancer, stomach cancer, liver cancer, and the like. Examples of infectious agents that infect the target cells can include the following: adenovirus, cytomegalovirus, Epstein-Barr virus, herpes simplex virus l, herpes simplex virus 2, human herpesvirus 6, varicella-zoster virus, hepatitis B virus, hepatitis D virus, papilloma virus, parvovirus B 19, polyomavirus BK, polyomavirus JC, hepatitis C virus, measles virus, rubella virus, human immunodeficiency virus (HIV), human T cell leukemia virus I, human T cell leukemia virus II, Chlamydia, Listeria, Salmonella, Legionella, Brucella, Coxiella, Rickettsia, Mycobacterium, Leishmania, Trypanasoma, Toxoplasma, Plasmodium, and the like.
Exemplary infectious agents and neoplastic cells are also included in Tables 1-5 below.
[0075] Furthermore the targets can include neoplastic cells described in or cells infected by agents that are described in any of the following references:
Jager, E. et al., "Granulocyte-macrophage-colony-stimulating factor enhances immune responses to melanoma-associated peptides in vivo," Int. J Cancer, 67:54-62 (1996); Kiindig, T.M., Althage, A., Hengartner, H. & Zinkernagel, R.M., "A skin test to assess CD8+ cytotoxic T
cell activity," Proc.
Natl. Acad Sci. USA, 89:7757-76 (1992); Bachmann, M.F. & Kundig, T.M., "In vitro vs. in vivo assays for the assessment of T- and B-cell function," Curr. Opin. Immunol., 6:320-326 (1994);
Kundig et al., "On the role of antigen in maintaining cytotoxic T cell memory," Proceedings of the National Academy of Sciences of the United States of America, 93:9716-23 (1996); Steinmann, R.M., "The dendritic cells system and its role in irnmunogenicity," Annual Review of Immunology 9:271-96 (1991); Inaba, K. et al., "Identification of proliferating dendritic cell precursors in mouse blood," Journal of Experimental Medicine, 175:1157-67 (1992); Young, J.W. &
Inaba, K., "Dendritic cells as adjuvants for class I major histocompatibility complex-restricted anti-tumor immunity," Journal of Experimental Medicine, 183:7-11 (1996); Kuby, Janis, Immunology, Second Edition, Chapter 15, W.H. Freeman and Company (1991); Austenst, E., Stahl, T., and de Gruyter, Walter, Insulin Pump Therapy, Chapter 3, Berlin, New York (1990);
Remington, The Science and Practice of Pharmacy, Nineteenth Edition, Chapters 86-88; Cleland, Jeffery L. and Langer, Robert (Editor), "Formulation and delivery of proteins and peptides,"
American Chemical Society (ACS Symposium Series, No. 567) (1994); Dickinson, Becton, which is fixed using Tegadenn transparent dressing TegadermTM 1624, 3M, St. Paul, MN 55144, USA;
Santus, Giancarlo and Baker, Richard, "Osmotic drug delivery: A review of the patent literature," Journal of Controlled Release, 35:1-21 (1995); Rammensee, U.S. Patent No. 5,747,269, issued May 05, 1998; Magruder, U.S. Patent No. 5,059,423, issued October 22, 1991; Sandbrook, U.S. Patent No.
4,552,651, issued November 25, 1985; Eckenhoff et al., U.S. Patent No.
3,987,790, issued October 26, 1976; Theeuwes, U.S. Patent No. 4,455,145, issued June 19, 1984; Roth et al. U.S. Patent No.
4,929,233, issued May 29 1990; van der Bruggen et al., U.S. Patent No.
5,554,506, issued September 10, 1996; Pfreundschuh, U.S. Patent No. 5,698,396, issued December 16, 1997;
Magruder, U.S. Patent No. 5,110,596, issued May 5, 1992; Eckenhoff, U.S.
Patent No. 4,619,652, issued October 28, 1986; Higuchi et al., U.S. Patent No. 3,995,631, issued December 07, 1976;
Maruyama, U.S. Patent No. 5,017,381, issued May 21, 1991; Eckenhoff, U.S.
Patent No.
4,963,141, issued October 16, 1990; van der Bruggen et al., U.S. Patent No.
5,558,995, issued September 24, 1996; Stolzenberg et al. U.S. Patent No. 3,604,417, issued September 14, 1971;
Wong et al., U.S. Patent No. 5,110,597, issued May 05, 1992; Eckenhoff, U.S.
Patent No.
4,753,651, issued June 28, 1988; Theeuwes, U.S. Patent No. 4,203,440, issued May 20, 1980;
Wong et al. U.S. Patent No. 5,023,088, issued June 11, 1991; Wong et al., U.S.
Patent No.
4,976,966, issued December 11, 1990; Van den Eynde et al., U.S. Patent No.
5,648,226, issued July 15, 199?; Baker et al., U.S. Patent No. 4,838,862, issued June 13, 1989;
Magruder, U.S.
Patent No. 5,135,523, issued August 04, 1992; Higuchi et al., U.S. Patent No.
3,732,865, issued May 15, 1975, ; Theeuwes, U.S. Patent No. 4,286,067, issued August, 25 1981;
Theeuwes et al., U.S. Patent No. 5,030,216, issued July 09, 1991; Boon et al., U.S. Patent No.
5,405,940, issued April 11, 1995; Faste, U.S. Patent No. 4,898,582, issued February 06, 1990;
Eckenhoff, U.S.
Patent No. 5,137,727, issued August 11, 1992; Higuchi et al., U.S. Patent No.
3,760,804, issued September 25, 1973; Eckenhoff et al., U.S. Patent No. 4,300,558, issued November 12, 1981;
Magruder et al., U.S. Patent No. 5,034,229, issued July 23, 1991; Boon et al., U.S. Patent No.
5,487,974, issued January 30, 1996; Kam et al., U.S. Patent No. 5,135,498, issued August 04, 1992; Magruder et al., U.S. Patent No. 5,174,999, issued December 29, 1992;
Higuchi, U.S.
Patent No. 3,760,805, September 25, 1973; Michaels, U.S. Patent No. 4,304,232, issued December 08, 1981; Magruder et al., U.S. Patent No. 5,037,420, issued October 15, 1991;
Wolfel et al., U.S.
Patent No. 5,530,096, issued June 25, 1996; Athadye et al., U.S. Patent No.
5,169,390, issued December 08, 1992; Balaban et al., U.S. Patent No. 5,209,746, issued May 11, 1993; Higuchi, U.S. Patent No. 3,929,132, issued December 30, 1975; Michaels, U.S. Patent No.
4,340,054, issued July 20, 1982; Magruder et al., U.S. Patent No. 5,057,318, issued October 15, 1991; Wolfel et al., U.S. Patent No. 5,519,117, issued May 21, 1996; Athadye et al., U.S.
Patent No. 5,257,987, issued November 02, 1993; Linkwitz et al., U.S. Patent No. 5,221,278, issued June 22, 1993;
Nakano et al., U.S. Patent No. 3,995,632, issued December 07, 1976; Michaels, U.S. Patent No.
4,367,741, issued January 11, 1983; Eckenhoff, U.S. Patent No. 4,865,598, issued September 12, 1989; Lethe et al., U.S. Patent No. 5,774,316, issued April 28, 1998;
Eckenhoff, U.S. Patent No.
4,340,048, issued July 20, 1982; Wong, U.S. Patent No. 5,223,265, issued June 29, 1993; Higuchi et al., U.S. Patent No. 4,034,756, issued July 12, 1977; Michaels, U.S. Patent No. 4,450,198, issued May 22, 1984; Eckenhoff et al., U.S. Patent No. 4,865,845, issued September 12, 1989;
Melief et. al., U.S. Patent No. 5,554,724, issued September 10, 1996;
Eckenhoff et al., U.S. Patent No. 4,474,575, issued October 02, 1984; Theeuwes, U.S. Patent No. 3,760,984, issued September 25, 1983; Eckenhoff, U.S. Patent No. 4,350,271, issued September 21, 1982;
Eckenhoff et al., U.S. Patent No. 4,855,141, issued August 08, 1989; Zingerman, U.S. Patent No.
4,872,873, issued October 10, 1989; Townsend et al., U.S. Patent No. 5,585,461, issued December 17, 1996;
Carulli, J.P. et al., J. Cellular Biochem Suppl., 30/31:286-96 (1998);
Tiireci, O., Sahin, U., and Pfreundschuh, M., "Serological analysis of human tumor antigens: molecular definition and implications," Molecular Medicine Today, 3:342 (1997); Rammensee et al., MHC
Ligands and Peptide Motifs, Landes Bioscience Austin, TX, 224-27, (1997); Parker et al., "Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains," J. Immunol. 152:163-175; Kido & Ohshita, Anal. Biochem., 230:41-47 (1995); Yamada et al., J. Biochem. (Tokyo), 95:1155-60 (1984); Kawashima et al., Kidney Int., 54:275-8 (1998);
Nakabayshi & Ikezawa, Biochem. Int. 16:1119-25 (1988); Kanaseki & Ohkuma, J.
Biochem.
(Tokyo), 110:541-7 (1991); Wattiaux et al., J. Cell Biol., 78:349-68 (1978);
Lisman et al., Biochem. J., 178:79-87 (1979); Dean, B., Arch. Biochem. Biophys., 227:154-63 (1983); Overdijk et al., Adv. Exp. Med. Biol., 101:601-10 (1978); Stromhaug et al., Biochem.
J., 335:217-24 (1998);
Escola et al., J. Biol. Chem., 271:27360-OS (1996); Hammond et al., Am. J.
Physiol., 267:F516-27 (1994); Williams & Smith, Arch. Biochem. Biophys., 305:298-306 (1993); Marsh, M., Methods Cell Biol., 31:319-34 (1989); Schmid & Mellman, Prog. Clin. Biol. Res., 270:35-49 (1988); Falk, K. et al., Nature, 351:290, (1991); Ausubel et al., Short Protocols in Molecular Biology, Third Edition, Unit 11.2 (1997); hypertext transfer protocol address 134.2.96.221/scripts/hlaserver.dll/EpPredict.htm; Levy, Morel, S. et al., Immunity 12:107-117 (2000); Seipelt et al., Virus Research, 62:159-68, 1999; Storkus et al., U.S.
Patent No. 5,989,565, issued November 23, 1999; Morton, U.S. Patent No. 5,993,828, issued November 30, 1999; Virus Research 62:159-168, (1999); Simard et al., U.S. Patent Application No.
10/026066, filed December 07, 2001; Simard et al., U.S. Patent Application No. 09/561571, filed April 28, 2000;
Simard et al., U.S. Patent Application No. 09/561572, filed April 28, 2000;
Miura et al., WO
99/01283, January 14, 1999; Simard et al., U.S. Patent Application No.
09/561074, filed April 28, 2000; Simard et al., U.S. Patent Application No. 10/225568, filed August 20, 2002; Simard et al., U.S. Patent Application No. 10/005905, filed November 07, 2001; Simard et al., U.S. Patent Application No. 09/561074, filed April 28, 2000.
[0076] Additional embodiments of the invention include methods, uses, therapies, and compositions relating to a particular antigen, whether the antigen is derived from, for example, a target cell or an infective agent, such as those mentioned above. Some preferred embodiments employ the antigens listed herein, in Tables 1-5, or in the list below, alone, as subsets, or in any combination. For example, some embodiments exclude use of one or more of those antigens.
Other embodiments may exclude any combination or all of those antigens.
Several examples of such antigens include MelanA (MART-I), gp100 (Pmel 17), tyrosinase, TRP-1, TRP-2, MAGE-1, MAGE-3, BAGS, GAGE-1, GAGE-2, CEA, RAGE, NY-ESO, SCP-1, Hom/Mel-40, PRAMS, p53, H-Ras, HER-2/neu, BCR-ABL, E2A-PRL, H4-RET, IGH-IGK, MYL-RAR, Epstein Ban virus antigens, EBNA, human papillomavirus (HPV) antigens E6 and E7, TSP-180, MAGE-4, MAGE-5, MAGE-6, p185erbB2, p180erbB-3, c-met, nm-23H1, PSA, TAG-72-4, CAM 17.1, NuMa, K-ras, (3-Catenin, CDK4, Mum-1, p16, as well as any of those set forth in the above mentioned references.
Other antigens are included in Tables 1-4 below.
[0077] Further embodiments include methods, uses, compositions, and therapies relating to epitopes, including, for example those epitopes listed in Tables 1-5. These epitopes can be useful to flank housekeeping epitopes in screening vectors, for example.
Some embodiments include one or more epitopes from Tables 1-5, while other embodiments specifically exclude one or more of such epitopes or combinations thereof.
Table 1 Virus Protein AA T cell epitope MHC molecule Position MHC ligand Anti en Adenovirus E3 9Kd 30-38 LIVIGILIL HLA-A*0201 SE . m N0.:44 Adenovirus EIA 234-243 SGPSNTPPEI H2-Db SE . )D N0.:45 Adenovirus E1B 192-200 VNIRNCCYI H2-Db (SE . ID N0.:46 Adenovirus EIA 234-243 SGPSNIPPEI T>I H2-Db SE . ID N0.:47 CSFV NS 2276-2284ENALLVALF SLA,haplotype of rotein d/d SE . ID N0.:48 Den a virusNS3 500-508 TPEGIIPTL HLA-B*3501 SE . ID N0.:49 EBV LMP-2 426-434 CLGGLLTMV HLA-A*0201 SE . ID N0.:50 EBV EBNA-1 480-484 NIAEGLRAL HLA-A*0201 SE .1D N0.:51 EBV EBNA-1 519-527 NLRRGTALA HLA-A*0201 SE . >D N0.:52 EBV EBNA-1 525-533 ALAIP CRL HLA-A*0201 SE .117 N0.:53 EBV EBNA-1 575-582 VLKDAIKDL HLA-A*0201 (SEQ. ID N0.:54) EBV EBNA-1 562-570 FMVFL THI HLA-A*0201 SE . m N0.:55 EBV EBNA-2 15-23 HLIVDTDSL HLA-A*0201 SE . B7 N0.:56 EBV EBNA-2 22-30 SLGNPSLSV HLA-A*0201 SE . ID N0.:57 EBV EBNA-2 126-134 PLASAMRML HLA-A*0201 SE . ID N0.:58) EBV EBNA-2 132-140 RMLWMANYI HLA-A*0201 SE . m N0.:59 EBV EBNA-2 133-141 MLWMANYN HL.A-A*0201 SE . ID N0.:60 EBV EBNA-2 151-159 ILPQGPQTA HLA-A*0201 SE . >D N0.:61 EBV EBNA-2 171-179 PLRPTAPTI HLA-A*0201 SE . ID N0.:62 EBV EBNA-2 205-213 PLPPATLTV HLA-A*0201 SE .1D N0.:63 EBV EBNA-2 246-254 RMHLPVLHV HLA-A*0201 SE . >D N0.:64 EBV EBNA-2 287-295 PMPLPPS L HLA-A*0201 (SEQ. ID N0.:65) EBV EBNA-2 294-302 LPPPAAPA HLA-A*0201 SE . ID N0.:66 EBV EBNA-2 381-389 SMPELSPVL HLA-A*0201 SE . ID N0.:67 EBV EBNA-2 453-461 DLDESWDYI HLA-A*0201 SE . ID N0.:68 EBV BZLFI 43-51 PLPCVLWPV HLA-A*0201 SE . ID N0.:69) EBV BZLFI 167-175 SLEECDSEL HLA-A*0201 SE . ID N0.:70 EBV BZLFl 176-t EIKRYKNRV HLA-A*OZOI
(SE . ID N0.:71) EBV BZLF1 195-203 QLL HYREV HLA-A*0201 (SE . ID N0.:72) EBV BZLFI 196-204 LL HYREVA HLA-A*0201 (SEQ. ID N0.:73 EBV BZLFI 217-225 LLK MCPSL HLA-A*0201 SE . 117 N0.:74 EBV BZLFI 229-237 SIIPRTPDV HLA-A*0201 SE . 117 N0.:75) EBV EBNA-6 284-293 LLDFVRFMGV HLA-A*0201 (SE . ID N0.:76 EBV EBNA-3 464-472 SVRDRLARL HLA-A*0203 SE . ID N0.:77 EBV EBNA-4 416-424 IVTDFSVIK HLA-A*1101 (SEQ. ID N0.:78 EBV EBNA-4 399-408 AVFDRKSDAK HLA-A*0201 (SE . B7 N0.:79 SE . ID N0.:80) SE . ID N0.:81) EBV EBNA-3 379-387 RPP1FIRRI. HLA-B7 SE . ID N0.:82 SEQ. ID N0.:83 SE . 117 N0.:84 SE . ID N0.:85 SE . ID N0.:86 EBV EBNA-1 72-80 R.P KRPSCI HLA-B7 SE . 117 N0.:87 SE . ID N0.:88) ( SEQ. ID N0.:89 SE . ID N0.:90 SE . ID N0.:91 SE . ID N0.:92 SE . ll~ N0.:93 SE . ID N0.:94 SE . ID N0.:9S
SE . ID N0.:96 (SE . ID N0.:97 SE . ID N0.:98 SE . 117 N0.:99 EBV LMP-2 236-244 RRRWRRLTV HLA-B*2704 SE . lD NO.:100 EBV EBNA-6 2S8-266 RRIYDLIEL HLA-B*2705 SE . ID NO.:101 EBV EBNA-3 4S8-466 YPLHE HGM HLA-B*3501 SEQ. )D NO.:102 EBV EBNA-3 4S8-466 YPLHE HGM HLA-B*3503 SEQ. ID NO.:103) SE . ID NO.:104 HCV env E 44-S1 ASRCWVAM HLA-B*3501 SE . 113 NO.: l OS
HCV core 27-3S G IVGGVYL HLA-B*40012 rotein SE . 117 N0.:106 HCV NSI 77-8S PPLTDFDQGW HLA-B*5301 SE . ID N0.:107 HCV core 18-27 LMGYIPLVGA H2-Dd rotein SEQ. ID NO.:108 HCV core 16-2S ADLMGYIPLV H2-Dd rotein SE . )D NO.:109 HCV NSS 409-424 MSYSWTGALVTPCAEE H2-Dd SE . ID NO.:110 HCV NS1 20S-213 KHPDATYSR Pa a-A06 SE . 117 NO.:111 HCV-1 NS3 400-409 KLVALGINAV HLA-A*0201 SEQ. ID NO.:112 HCV-1 NS3 440-448 GDFDSV~C Patr-B16 SE . )I7 N0.:113 HCV-1 env E 118-126 GNASRCWVA Patr-BI6 SE . ID NO.:114 HCV-1 NSI 1S9-167 TRPPLGNWF Patr-B13 SE . >D NO.:11 S
HCV-1 NS3 3S1-3S9 VPHPNIEEV Patr-B13 SE . ll~ NO.:116 HCV-1 ~~ NS3 438-446 YTGDFDSVI Patr-BO1 _ SE . ID N0.:117 HCV-1 NS4 328-335 SWAIKWEY Patr-All SEQ. ~ NO.:118 HCV-1 NSI 205-213 KHPDATYSR Patr-A04 SE . ID N0.:119 HCV-1 NS3 440-448 GDFDSVIDC Patr-A04 SEQ. ID N0.:120 SEQ. ID NO.:121 HIV a 24 267-275 IVGLNKNR HLA-A*3302 (SEQ. ID N0.:122) HIV a 24 262-270 EIYKRWIIL HLA-B8 (SEQ. ID NO.:123 HIV a 24 261-269 GEIYKRWII HLA-B8 SE . ID NO.:124 HIV a 17 93-101 EIKDTKEAL HLA-B8 SEQ. ID NO.:125 SEQ. ID N0.:126 HIV a 24 267-277 ILGLNKIVRMY HLA-B* 1501 (SEQ. ID N0.:127 SEQ. ILl N0.:128 HIV nef 115-125 YHTQGYFPQWQ HLA-B 17 SE . ID NO.:129 HIV nef 117-128 TQGYFPQWQNYT HLA-B17 SE . ID N0.:130 HIV I20 314-322 GRAFVT1GK HLA-B*2705 (SEQ. ID N0.:131 HIV a 24 263-271 KRWIII,GLN HLA-B*2702 SEQ. m NO.:132 HIV nef 72-82 VPLRPMTYK HLA-B*3501 SEQ. ID N0.:133 HIV nef 117-125 TQGYFP W HLA-B*3701 SE . ID NO.:134 HIV a 24 143-151 HQAISPRTI, HLA-Cw*0301 SEQ. ID NO.:135 HIV a 24 140-151 QMVH AISPRTL HLA-Cw*0301 SEQ, m N0.:136 HIV 120 431-440 MYAPPIGG I H2-Kd SE .117 N0.:137 HIV 160 318-327 RGPGRAFVTI H2-Dd SE . ll7 N0.:138 HIV 120 17-29 MPGRAFVTI H2-Ld SEQ. ID N0.:139 HIV-1 RT 476-484 LKEPVHGV HLA-A*0201 I
SE . ID N0.:140 HIV-1 nef 190-198 AFHHVAREL HLA-A*0201 SEQ. ID N0.:141 HIV-1 I60 120-128 KLTPLCVTL HLA-A*0201 SE . ID NO.:142 HIV-1 60 814-823 SLLNATDIAV HLA-A*0201 SE . ID NO.:143) HIV-1 RT 179-187 MY YMDDL HLA-A*0201 SE . 117 N0.:144 HIV-1 a 17 77-85 SLYNTVATL HLA-A*0201 SE . ID NO.:145) HIV-1 160 315-329 RGPGRAFVT1 HLA-A*0201 SE . ID NO.:146) SE .117 N0.:147 HIV-1 nef 73-82 VPLRPMTYK HLA-A3 SE . 117 NO.:148) SE . ID N0.:149) HIV-1 a 17 20-29 RLRPGGKKK HLA-A3 SE . ID NO.:150 SE . ID NO.:151 HIV-1 nef 74-82 VPLRPMTYK HLA-a* 11 SE . ID N0.:152 HIV-1 a 24 325-333 AIF SSMTK HLA-A*1101 SE . 117 NO.:153 HIV-1 nef 73-82 VPLRPMTYK HLA-A* 1101 SEQ. ID NO.:154 HIV-1 nef 83-94 AAVDLSHFLKEK HLA-A*1101 SE . ID NO.:155 HIV-1 a 24 349-359 AC GVGGPGGHK HLA-A*1101 SEQ. ID N0.:156 HIV-1 a 24 203-212 ETINEEAAEW HLA-A25 SE . ID N0.:157 HIV-1 nef 128-137 TPGPGVRYPL HLA-B7 SE . ID N0.:158 HIV-1 a 17 24-31 GGKKKYKL HLA-B8 SE . ID N0.:159 SEQ. ID NO.:160 HIV-1 a 24 298-306 DRFYKTLRA HLA-B 14 SE . II7 N0.:161 SE . ID NO.:162 HIV-1 a 24 265-24 KRWIII,GLNK HLA-B*2705 SEQ. ID NO.:163 HIV-1 nef 190-198 AFHHVAREL HLA-B*5201 SE . ll~ NO.:164 SE . 117 NO.:165 EBV EBNA-6 130-139 EENLLDFVRF HLA-B*4403 SE . ID NO.:166 _ I - ~ - - (SEQ. ID NO.:167) SE . m N0.:168 SE . >D N0.:169 HBV sA 348-357 GLSPTVWLSV HLA-A*0201 SE . ID NO.:170 HBV SA 335-343 WLSLLVPFV HLA-A*0201 SE . )D NO.:171 HBV cA 18-27 FLPSDFFPSV HLA-A*0201 SEQ. ID N0.:172) HBV cA 18-27 FLPSDFFPSV HLA-A*0202 SE . ID NO.:173 HBV cA 18-27 FLPSDFFPSV HLA-A*0205 SE . ID NO.:174 HBV cA 18-27 FLPSDFFPSV HLA-A*0206 SE . ID N0.:175) HBV of 575-583 FLLSLGIHL HLA-A*0201 SE . ID NO.:176 HBV of 816-824 SLYADSPSV HLA-A*0201 SE . ID NO.:177 HBV of 455-463 GLSRYVARL HLA-A*0201 SE . ID NO.:178 HBV env 338-347 LLVPFV WFV HLA-A*0201 SEQ. ID NO.:179) HBV of 642-650 ALMPLYACI HLA-A*0201 SEQ. ID NO.:180 HBV env 378-387 LLPIFFCLWV HLA-A*0201 SE . )D N0.:181 HBV of 538-546 YMDDVVLGA HLA-A*0201 SE . B7 NO.:182 HBV env 250-258 LLLCLIFLL HLA-A*0201 SEQ. ID N0.:183 HBV env 260-269 LLDYQGMLPV HLA-A*0201 SE . ID NO.:184 HBV env 370-379 SNSPFIPLL HLA-A*0201 SE . ID N0.:185 HBV env 183-191 FLLTRILTI HLA-A*0201 SE . ID NO.:186 HBV cA 88-96 YVNVNMGLK HLA-A* 1101 SEQ. ID N0.:187 HBV cA 141-151 STLPETTVVRR HLA-A*3101 SEQ. ID N0.:188 HBV eA 141-151 STLPETTVVRR HLA-A*6801 SE . ID N0.:189 HBV cA 18-27 FLPSDFFPSV HLA-A*6801 SE . ID NO.:190 HBV sA 28-39 IP SLDSWWTSL H2-Ld SEQ. )D NO.:191 HBV cA 93-100 MGLKFR L H2-Kb SE .117 NO.:l92 ~V ~ preS ~ 141-149~ STBXQSGXQ ~ HLA-A*0201 SE . ID N_O.:193 HCMV B 618-628 FIAGNSAYEYV HLA-A*0201 SE . ID N0.:194 SE . ID NO.:195 HCMV 65 397-411 DDVWTSGSDSDEELV HLA-b35 SE . ID NO.: I
HCMV 65 123-131 IPSINVHHY HLA-B*3501 SE . ID NO.:197) HCMV 65 495-504 NLVPMVATVO HLA-A*0201 SE . ID N0.:198 SE . ID NO.:199 HCV MP 17-25 DLMGYIPLV HLA-A*0201 SE . ID N0.:200 HCV MP 63-72 LLALLSCLTV HLA-A*0201 SEQ. ID N0.:201 HCV MP 105-112 ILHTPGCV HLA-A*0201 SE . ID N0.:202 HCV env E 66-75 LRRHIDLLV HLA-A*0201 SE . 117 N0.:203 HCV env E 88-96 DLCGSVFLV HLA-A*0201 SE . ID N0.:204 HCV env E 172-180 SMVGNWAKV HLA-A*0201 SEQ. ID N0.:205 HCV NSI 308-316 HLII NNDV HLA-A*0201 SE . ID N0.:206) HCV NSI 340-348 FLLLADARV HLA-A*0201 SEQ. ID N0.:207 HCV NS2 234-246 GLRDLAVAVEPVV HLA-A*0201 SE .11? N0.:208 HCV NSI 18-28 SLLAPGAKQNV HLA-A*0201 SE . D7 N0.:209 HCV NSI 19-28 LLAPGAK NV HLA-A*0201 SEQ. ID N0.:210 HCV NS4 192-201 LLFNILGGWV HLA-A*0201 SE . ID N0.:211 HCV NS3 579-587 YLVAY ATV HLA-A*0201 SE . ID N0.:212 HCV core 34-43 YLLPRRGPRL HLA-A*0201 rotein SE . ID N0.:213 HCV MP 63-72 LLALLSCLTI HLA-A*0201 SE . ID N0.:214) HCV NS4 174-182 SLMAFTAAV HLA-A*0201 SEQ. ID N0.:21 S
HCV NS3 67-75 CINGVCWTV HLA-A*0201 SE . ID N0.:216 HCV NS3 163-171 LLCPAGHAV HLA-A*0201 SE . ID N0.:217 HCV NS5 239-247 IL,DSFDPLV HLA-A*0201 SE .117 N0.:218 HCV NS4A 236-244 ILAGYGAGV HLA-A*0201 SE . ID N0.:219) HCV NSS 714-722 GL DCTMLV HLA-A*0201 (SE . ID N0.:220 HCV NS3 281-290 TGAPVTYSTY HLA-A*0201 SEQ. ID N0.:221 HCV NS4A 149-157 HMWNFISGI HLA-A*0201 SE . B7 N0.:222 HCV NSS 575-583 RVCEKMALY HLA-A*0201-A3 (SEQ. ID N0.:223) HCV NS1 238-246 TINYTIFK HLA-A*1101 SEQ. ID N0.:224) SEQ. ID N0.:225 HCV core 40-48 GPRLGVRAT HLA-B7 rotein SE .117 N0.:226 HIV-1 120 380-388 SFNCGGEFF HLA-Cw*0401 (SEQ. ID N0.:227 HIV-1 RT 206-214 TEMEKEGKI H2-Kk SE . ID N0.:228) HIV-1 17 18-26 KIRLRPGGK HLA-A*0301 SEQ. ID N0.:229 HIV-1 P17 20-29 RLRPGGKKKY HLA-A*0301 (SEQ. ID N0.:230 HIV- I RT 325-333 AIFQSSMTK HLA-A*0301 SE . ID N0.:231) SE . ID N0.:232 HIV-1 RT 508-517 IYQEPFKNLK HLA-All (SEQ. ID N0.:233 (SEQ. ID N0.:234) SEQ. ID N0.:235) HN-1 a 24 145-155 QAISPRTLNAW HLA-A25 SE . ID N0.:236 HN-1 a 24 167-175 EVIPMFSAL HLA-A26 SEQ. >I7 N0.:237 (SEQ. ID N0.:238 SEQ. ID N0.:239) SEQ. ID N0.:240 (SEQ. ID N0.:241 HIV-1 RT 71-79 ITLWQRPLV HLA-A*6802 SE . ID N0.:242 HIV-1 RT 85-93 DTVLEEMNL HLA-A*6802 SEQ.117 N0.:243 HIV-1 RT 71-79 ITLW RPLV HLA-A*7401 SE .1T7 N0.:244 HIV-1 a 24 148-156 SPRTLNAWV HLA-B7 SE . a? N0.:245 HIV-1 a 24 179-187 ATP DLNTM HLA-B7 SE .1D N0.:246 SE . >D N0.:247 HIV-1 41 ~ 843-8S1 IPRRIRQGL HLA-B7 SE . ~ N0.:248 SE . m N0.:249 HIV-1 nef 13-20 WPTVRERM HLA-B8 SE . ID N0.:2S0 HIV-1 nef 90-97 FLKEKGGL HLA-B8 SE . ID N0.:2S 1 ~-1 a 24 183-191 DLNTMLNTV HLA-B14 SE . B7 N0.:252 SE . ID N0.:253 SE .1D N0.:254 SE . ID N0.:255 HN-1 nef 73-82 VPLRPMTYK HLA-B27 SE . m N0.:2Sb SE . ID N0.:2S7 HIV-1 nef 105-114 RR DILDLWI HLA-B*2705 SE . ~ N0.:2S8) HIV-1 nef 134-141 RYPLTFGW HLA-B*2705 SEQ. ID N0.:2S9 SEQ. m N0.:260 SE . lZ7 N0.:261 ~-1 120 42-S2 VPVWKEATTTL HLA-B3S
SE . m N0.:262 SE . ID N0.:263 HIV-1 a 24 2S4-262 PPIPVGDIY HLA-B35 SE , m N0.:264 SE . ~ N0.:265) SE . ID N0.:266 HIV-1 a 2 45-253 NPVPVGNIY HLA-B3S
SE . ll~ N0.:267 ~-1 n ef 1 20-128 FPDWQNYT HLA-B37 Y
SE . ID N0.:268 HIV-1 a 24 1 93-201 H AAM ML HLA-B42 G
SE . m N0.:269 WO 2003/063770 PCT/US2002/036(19R
SE . ID N0.:270) SE . ID N0.:271 SE . ID N0.:272) _ HN-1 a 24 325-333 NANPDCKTI HLA-BS I
SE . ID N0.:273 HN-1 a 24 275-282 RMYSPTSI HLA-BS2 SEQ. ID N0.:274) HN-I 120 42-S1 VPVWKEATTT HLA-B*5501 SE . ID N0.:275) HN-I a 24 147-1SS ISPRTLNAW HLA-B57 (SE . ID N0.:276 HN-1 a 24 240-249 TSTL E IGW HLA-BS7 (SE .117 N0.:277) HIV-I a 24 162-172 KAFSPEVIPMF HLA-BS7 SE . ID N0.:278 HIV-1 a 24 311-319 ASQEVKNW HLA-BS7 SE . ID N0.:279 HIV-1 a 24 311-319 QAS DVKNW HLA-B57 SEQ. ID N0.:280 HN-1 nef 116-12S HT GYFPDW HLA-BS7 SEQ. ID N0.:281) HIV-1 nef 120-128 YFPDWQNYT HLA-BS7 (SE .117 N0.:282 HIV-1 a 24 240-249 TSTLQEQIGW HLA-BS8 SE . ID N0.:283) SE . ID N0.:284 SEQ. m N0.:285 (SEQ. m N0.:286 SE .117 N0.:287) HN-1 nef 117-127 TQGYFPDW NY HLA-B62 SE .117 N0.:288) HIV-1 nef 84-91 AVDLSHFL HLA-B62 SEQ. >I? N0.:289 HIV-1 a 24 168-175 VIPMFSAL H LA-Cw*0102 ( SEQ. m N0.:290 F
SE . ll7 N0.:291 HN-1 120 3?S-383 FNCGGEFF H LA-B1S
S
SE . m N0.:292 HIV-1 n ef 1 36-14S LTFGWCYKL H LA-A*0201 P
SE . ID N0.:293 HIV-1 n ef 1 80-189 LEWRFDSRL H LA-A*0201 V
SE . ID N0.:294 HN-1 n ef 6 8-77 PVTP VPLR H LA-B7 F
1 S [0020] Another embodiment of the disclosed invention relates to vectors including a housekeeping epitope expression cassette. The housekeeping epitope(s) can be derived from a target-associated antigen, and the housekeeping epitope can be liberatable, that is capable of liberation, from a translation product of the cassette by immunoproteasome processing.
[0021] In one aspect of the invention the expression cassette can encode an array of two or more epitopes or at least one epitope and at least one epitope cluster.
The members of the array can be arranged head-to-tail, for example. Also, the members of the array can be arranged head-to-tail separated by spacing sequences, for example. Further, the array can include a plurality of housekeeping epitopes. The plurality of housekeeping epitopes can include more than one copy of the same epitope or single copies of distinct epitopes, for example. The array can include at least one housekeeping epitope and at least one immune epitope. Also, the array can include alternating housekeeping and immune epitopes. Further, the array includes a housekeeping epitope sandwiched between two immune epitopes so that there are two immune epitopes between each housekeeping epitope in the interior of the array. The immune epitopes can be truncated distally to their junction with the adjacent housekeeping epitope.
[0022] In another aspect, the expression cassette further encodes an authentic protein sequence, or segment thereof, including at least one immune epitope.
Optionally, the segment can include at least one epitope cluster. The housekeeping epitope expression cassette and the authentic sequence including at least one immune epitope can be encoded in a single reading frame or transcribed as a single mRNA species, for example. Also, the housekeeping epitope expression cassette and the authentic sequence including at least one immune epitope may not be transcribed as a single mRNA species.
[0023) In yet another aspect, the vector can include a DNA molecule or an RNA
molecule. The vector can encode, for example, SEQ )D NO. 4, SEQ 117 NO. 17, SEQ )D NO. 20, SEQ ID NO. 26, SEQ Il7'NO. 27, SEQ ID NO. 29, SEQ ID NO. 33, and the like.
Also, the vector can include SEQ >I7 NO. 9, SEQ ID NO. 19, SEQ >D NO. 21, SEQ ID NO. 30, SEQ ID
NO. 34, and the like. Also, the vector can encode SEQ ID NO. 5 or SEQ I17 NO. 18, for example.
[0024] In still another aspect, the target-associated antigen can be an antigen derived from or associated with a tumor or an intracellular parasite, and the intracellular parasite can be, for example, a virus, a bacterium, a protozoan, or the like.
[0025] Another embodiment of the invention relates to vectors including a housekeeping epitope identified according to any of the methods disclosed herein, claimed or otherwise. For example, embodiments can relate to vector encoding a substrate polypeptide that includes a housekeeping epitope by any of the methods described herein.
[0026) In one aspect, the housekeeping epitope can be liberated from the cassette translation product by immune proteasome processing [0027] Another embodiment of the disclosed invention relates to methods of activating a T cell. The methods can include, for example, the steps of contacting a vector including a housekeeping epitope expression cassette with an APC. The housekeeping epitope can be derived from a target-associated antigen, for example, and the housekeeping epitope can be liberatable from a translation product of the cassette by immunoproteasome processing. The methods can further include contacting the APC with a T cell. The contacting of the vector with the APC can occur in vitro or in vivo.
[0028] Another embodiment of the disclosed invention relates to a substrate polypeptide including a housekeeping epitope wherein the housekeeping epitope can be liberated by immunoproteasome processing in a pAPC.
[0029] Another embodiment of the disclosed invention relates to a method of activating a T cell comprising contacting a substrate polypeptide including a housekeeping epitope with an APC wherein the housekeeping epitope can be liberated by immunoproteasome processing and contacting the APC with a T cell.
Brief Description of the Drawings [0030] Figure 1. An illustrative drawing depicting pMA2M.
[0031] Figure 2. Assay results showing the % of specific lysis of ELAGIGII,TV
pulsed and unpulsed T2 target cells by mock immunized CTL.
[0032) Figure 3. Assay results showing the % of specific lysis of ELAGIGILTV
pulsed and unpulsed T2 target cells by pVAXM3 immunized CTL.
[0033] Figure 4. Assay results showing the % of specific lysis of ELAGIGIL,TV
pulsed and unpulsed T2 target cells by pVAXM2 immunized CTL.
[0034] Figure S. Assay results showing the % of specific lysis of ELAGIGILTV
pulsed and unpulsed T2 target cells by pVAXMl immunized CTL.
[0035] Figure 6. Illustrates a sequence of SEQ m NO. 22 from which the NY-ESO-1 is~abs epitope is liberated by immunoproteasomal processing.
[0036] Figure 7. Shows the differential processing by immunoproteasome and housekeeping proteasome of the SLLMWITQC epitope (SEQ ID NO. 12) in its native context where the cleavage following the C is more efficiently produced by housekeeping than immunoproteasome.
[0037] Figure 8. 8A: Shows the results of the human immunoproteasome digest of SEQ 117 NO. 31. 8B: Shows the comparative results of mouse versus human immunoproteasome digestion of SEQ ID NO. 31.
[0038] Figure 9. Shows the differential processing of SSX-23,_68 by housekeeping and immunoproteasome.
Detailed Description of the Preferred Embodiment Definitions [0039] Unless otherwise clear from the context of the use of a term herein, the following listed terms shall generally have the indicated meanings for purposes of this description.
[0040] PROFESSIONAL ANTIGEN-PRESENTING CELL (pAPC) - a cell that possesses T cell costimulatory molecules and is able to induce a T cell response. Well characterized pAPCs include dendritic cells, B cells, and macrophages.
[0041] PERIPHERAL CELL - a cell that is not a pAPC.
[0042] HOUSEKEEPING PROTEASOME - a proteasome normally active in peripheral cells, and generally not present or not strongly active in pAPCs.
[0043] IMMUNOPROTEASOME - a proteasome normally active in pAPCs; the immunoproteasome is also active in some peripheral cells in infected tissues or following exposure to interferon.
[0044] EPITOPE - a molecule or substance capable of stimulating an immune response. In preferred embodiments, epitopes according to this definition include but are not necessarily limited to a polypeptide and a nucleic acid encoding a polypeptide, wherein the polypeptide is capable of stimulating an immune response. In other preferred embodiments, epitopes according to this definition include but are not necessarily limited to peptides presented on the surface of cells, the peptides being non-covalently bound to the binding cleft of class I MHC, such that they can interact with T cell receptors (TCR). Epitopes presented by class I MHC may be in immature or mature form. "Mature" refers to an MHC epitope in distinction to any precursor ("immature") that may include or consist essentially of a housekeeping epitope, but also includes other sequences in a primary translation product that are removed by processing, including without limitation, alone or in any combination, proteasomal digestion, N-terminal trimming, or the action of exogenous enzymatic activities. Thus, a mature epitope may be provided embedded in a somewhat longer polypeptide, the immunological potential of which is due, at least in part, to the embedded epitope; or in its ultimate form that can bind in the MHC binding cleft to be recognized by TCR, respectively.
[0045] MHC EPITOPE - a polypeptide having a known or predicted binding affinity for a mammalian class I or class II major histocompatibility complex (MHC) molecule.
[0046] HOUSEKEEPING EPITOPE - In a preferred embodiment, a housekeeping epitope is defined as a polypeptide fragment that is an MHC epitope, and that is displayed on a cell in which housekeeping proteasomes are predominantly active. In another preferred embodiment, a housekeeping epitope is defined as a polypeptide containing a housekeeping epitope according to the foregoing definition, that is flanked by one to several additional amino acids. In another preferred embodiment, a housekeeping epitope is defined as a nucleic acid that encodes a housekeeping epitope according to the foregoing definitions. Exemplary housekeeping epitopes are provide in U.S. Application No. 10/117,937, filed on April 4, 2002; and U.S. Provisional Application Nos. 60/282,211, filed on April 6, 2001; 60/337,017, filed on November 7, 2001;
60/363210 filed 3/7/02; and 60/409,123, filed on September 5, 2002; all of which are entitled EPITOPE SEQUENCES.
[0047) IMMUNE EPITOPE - In a preferred embodiment, an immune epitope is defined as a polypeptide fragment that is an MHC epitope, and that is displayed on a cell in which immunoproteasomes are predominantly active. In another preferred embodiment, an immune epitope is defined as a polypeptide containing an immune epitope according to the foregoing definition, that is flanked by one to several additional amino acids. In another preferred embodiment, an immune epitope is defined as a polypeptide including an epitope cluster sequence, having at least two polypeptide sequences having a known or predicted affinity for a class I MHC.
In yet another preferred embodiment, an immune epitope is defined as a nucleic acid that encodes an immune epitope according to any of the foregoing definitions.
[0048] TARGET CELL - a cell to be targeted by the vaccines and methods of the invention. Examples of target cells according to this definition include but are not necessarily limited to: a neoplastic cell and a cell harboring an intracellular parasite, such as, for example, a virus, a bacterium, or a protozoan. Target cells can also include cells that are targeted by CTL as a part of assays to determine or confirm proper epitope liberation and processing by a cell expressing immunoproteasome, to determine T cell specificity or immunogenicity for a desired epitope.. Such cells may be transfored to express the substrate or liberation sequence, or the cells can simply be pulsed with peptidelepitope.
[0049] TARGET-ASSOCIATED ANTIGEN (TAA) - a protein or polypeptide present in a target cell.
[0050] TUMOR-ASSOCIATED ANTIGENS (TuAA) - a TAA, wherein the target cell is a neoplastic cell.
[0051) HLA EPITOPE - a polypeptide having a known or predicted binding affinity for a human class I or class II HLA complex molecule.
[0052] ANTIBODY - a natural immunoglobulin (Ig), poly- or monoclonal, or any molecule composed in whole or in part of an Ig binding domain, whether derived biochemically or by use of recombinant DNA. Examples include inter alia, F(ab), single chain Fv, and Ig variable region-phage coat protein fusions.
[0053] ENCODE - an open-ended term such that a nucleic acid encoding a particular amino acid sequence can consist of codons specifying that (poly)peptide, but can also comprise additional sequences either translatable, or for the control of transcription, translation, or replication, or to facilitate manipulation of some host nucleic acid construct.
[0054] SUBSTANTIAL SIMILARITY - this term is used to refer to sequences that differ from a reference sequence in an inconsequential way as judged by examination of the sequence. Nucleic acid sequences encoding the same amino acid sequence are substantially similar despite differences in degenerate positions or modest differences in length or composition of any non-coding regions. Amino acid sequences differing only by conservative substitution or minor length variations are substantially similar. Additionally, amino acid sequences comprising housekeeping epitopes that differ in the number of N-terminal flanking residues, or immune epitopes and epitope clusters that differ in the number of flanking residues at either terminus, are substantially similar. Nucleic acids that encode substantially similar amino acid sequences are themselves also substantially similar.
[0055] FUNCTIONAL SIMILARITY - this term is used to refer to sequences that differ from a reference sequence in an inconsequential way as judged by examination of a biological or biochemical property, although the sequences may not be substantially similar. For example, two nucleic acids can be useful as hybridization probes for the same sequence but encode differing amino acid sequences. Two peptides that induce cross-reactive CTL
responses are functionally similar even if they differ by non-conservative amino acid substitutions (and thus do not meet the substantial similarity definition). Pairs of antibodies, or TCRs, that recognize the same epitope can be functionally similar to each other despite whatever structural differences exist.
In testing for functional similarity of immunogenicity one would generally immunize with the "altered" antigen and test the ability of the elicited response (Ab, CTL, cytokine production, etc.) 3 5 to recognize the target antigen. Accordingly, two sequences may be designed to differ in certain _g_ respects while retaining the same function. Such designed sequence variants are among the embodiments of the present invention.
[0056] EXPRESSION CASSETTE - a polynucleotide sequence encoding a polypeptide, operably linked to a promoter and other transcription and translation control elements, including but not limited to enhancers, termination codons, internal ribosome entry sites, and polyadenylation sites. The cassette can also include sequences that facilitate moving it from one host molecule to another.
[0057) EMBEDDED EPITOPE - an epitope contained within a longer polypeptide, also can include an epitope in which either the N- terminus or the C-terminus is embedded such that the epitope is not in an interior position.
[0058] MATURE EPITOPE - a peptide with no additional sequence beyond that present when the epitope is bound in the MHC peptide-binding cleft.
[0059] EPITOPE CLUSTER - a polypeptide, or a nucleic acid sequence encoding it, that is a segment of a native protein sequence comprising two or more known or predicted epitopes with binding affinity for a shared MHC restriction element, wherein the density of epitopes within the cluster is greater than the density of all known or predicted epitopes with binding affinity for the shared MHC restriction element within the complete protein sequence, and as disclosed in U.S.
Patent Application No. 09/561,571 entitled EPITOPE CLUSTERS.
[0060] Substrate or liberation sequence- a designed or engineered sequence comprising or encoding a housekeeping epitope (according to the first of the definitions offered above) embedded in a larger sequence that provides a context allowing the housekeeping epitope to be liberated by immunoproteasomal processing, directly or in combination with N-terminal trimming or other processes.
[0061) Degradation of cytosolic proteins takes place via the ubiquitin-dependent multi-catalytic multi-subunit protease system known as the proteasome. The proteasome degrades cytosolic proteins generating fragments that can then be translocated from the cytosol into the endoplasmic reticulum (ER) for loading onto class I MHC. Such protein fragments shall be referred to as class I peptides. The peptide loaded MHC are subsequently transported to the cell surface where they can be detected by CTL.
[0062] The mufti-catalytic activity of the proteasome is the result of its mufti-subunit structure. Subunits are expressed from different genes and assembled post-translationally into the proteasome complex. A key feature of the proteasome is its bimodal activity, which enables it to exert its protease, or cleavage function, with two discrete kinds of cleavage patterns. This bimodal action of the proteasome is extremely fundamental to understanding how CTL are targeted to recognize peripheral cells in the body and how this targeting requires synchronization between the immune system and the targeted cells.
[0063] The housekeeping proteasome is constitutively active in all peripheral cells and tissues of the body. The first mode of operation for the housekeeping proteasome is to degrade cellular protein, recycling it into amino acids. Proteasome function is therefore a necessary activity for cell life. As a corollary to its housekeeping protease activity, however, class I peptides generated by the housekeeping proteasome are presented on all of the peripheral cells of the body.
[0064] The proteasome's second mode of function is highly exclusive and occurs specifically in pAPCs or as a consequence of a cellular response to interferons (IFNs). In its second mode of activity the proteasome incorporates unique subunits, which replace the catalytic subunits of the constitutive housekeeping proteasome. This "modified"
proteasome has been called the immunoproteasome, owing to its expression in pAPC and as a consequence of induction by IFN
in body cells.
[0065] APC define the repertoire of CTL that recirculate through the body and are potentially active as killer cells. CTL are activated by interacting with class I peptide presented on the surface of a pAPC. Activated CTL are induced to proliferate and caused to recirculate through the body in search of diseased cells. This is why the CTL response in the body is defined specifically by the class I peptides produced by the pAPC. It is important to remember that pAPCs express the immunoproteasome, and that as a consequence of the bimodal activity of the proteasome, the cleavage pattern of proteins (and the resultant class I
peptides produced) are different from those in peripheral body cells which express housekeeping proteasome. The differential proteasome activity in pAPC and peripheral body cells, therefore, is important to consider during natural infection and with therapeutic CTL vaccination strategies.
[0066] All cells of the body are capable of producing IFN in the event that they are infected by a pathogen such as a virus. IFN production in turn results in the expression of the immunoproteasome in the infected cell. Viral antigens are thereby processed by the immunoproteasome of the infected cell and the consequent peptides are displayed with class I
MHC on the cell surface. At the same time, pAPC are sequestering virus antigens and are processing class I peptides with their immunoproteasome activity, which is normal for the pAPC
cell type. The CTL response in the body is being stimulated specifically by the class I peptides produced by the pAPC. Fortunately, the infected cell is also producing class I
peptides from the immunoproteasome, rather than the normal housekeeping proteasome. Thus, virus-related class I
peptides are being produced that enable detection by the ensuing CTL response.
The CTL immune response is induced by pAPC, which normally produce different class I peptides compared to peripheral body cells, owing to different proteasome activity. Therefore, during infection there is epitope synchronization between the infected cell and the immune system.
[0067] This is not the case with tumors and chronic viruses, which block the interferon system. For tumors there is no infection in the tumor cell to induce the immunoproteasome expression, and chronic virus infection either directly or indirectly blocks immunoproteasome expression. In both cases the diseased cell maintains its display of class I
peptides derived from housekeeping proteasome activity and avoids effective surveillance by CTL.
[0068) In the case of therapeutic vaccination to eradicate tumors or chronic infections, the bimodal function of the proteasome and its differential activity in APC
and peripheral cells of the body is significant. Upon vaccination with protein antigen, and before a CTL response can occur, the antigen must be acquired and processed into peptides that are subsequently presented on class I MHC on the pAPC surface. The activated CTL recirculate in search of cells with similar class I peptide on the surface. Cells with this peptide will be subjected to destruction by the cytolytic activity of the CTL. If the targeted diseased cell does not express the immunoproteasome, which is present in the pAPC, then the epitopes are not synchronized and CTL
fail to find the desired peptide target on the surface of the diseased cell.
[0069] Preferably, therapeutic vaccine design takes into account the class I
peptide that is actually present on the target tissue. That is, effective antigens used to stimulate CTL to 1 S attack diseased tissue are those that are naturally processed and presented on the surface of the diseased tissue. For tumors and chronic infection this generally means that the CTL epitopes are those that have been processed by the housekeeping proteasome. Tn order to generate an effective therapeutic vaccine, CTL epitopes are identified based on the knowledge that such epitopes are, in fact, produced by the housekeeping proteasome system. Once identified, these epitopes, embodied as peptides, can be used to successfully immunize or induce therapeutic CTL
responses against housekeeping proteasome expressing target cells in the host.
[0070] However, in the case of DNA vaccines, there can be an additional consideration. The immunization with DNA requires that APCs take up the DNA
and express the encoded proteins or peptides. It is possible to encode a discrete class I
peptide on the DNA. By immunizing with this construct, APCs can be caused to express a housekeeping epitope, which is then displayed on class I MHC on the surface of the cell for stimulating an appropriate CTL
response. Constructs for generation of proper termini of housekeeping epitopes have been described in U.S. Patent application No. 09/561,572 entitled EXPRESSION
VECTORS
ENCODING EPITOPES OF TARGET-ASSOCIATED ANTIGENS, filed on April 28, 2000.
[0071) Embodiments of the invention provide expression cassettes that encode one or more embedded housekeeping epitopes, and methods far designing and testing such expression cassettes. The expression cassettes and constructs can encode epitopes, including housekeeping epitopes, derived from antigens that are associated with targets. Housekeeping epitopes can be liberated from the translation products) of the cassettes. For example, in some embodiments of 3 5 the invention, the housekeeping epitope(s) can be flanked by arbitrary sequences or by sequences incorporating residues known to be favored in immunoproteasome cleavage sites.
In further embodiments of the invention multiple epitopes can be arrayed head-to-tail. In some embodiments, these arrays can be made up entirely of housekeeping epitopes. Likewise, the arrays can include alternating housekeeping and immune epitopes. Alternatively, the arrays can include housekeeping epitopes flanked by immune epitopes, whether complete or distally truncated.
In some preferred embodiments, each housekeeping epitope can be flanked on either side by an immune epitope, such that an array of such arrangements has two immune epitopes between each housekeeping epitope.
Further, the arrays can be of any other similar arrangement. There is no restriction on placing a housekeeping epitope at the terminal positions of the array. The vectors can additionally contain authentic protein coding sequences or segments thereof containing epitope clusters as a source of immune epitopes.
[0072] Several disclosures make reference to polyepitopes or string-of bead arrays.
See, for example, W00119408A1, March 22, 2001; W09955730A2, November 4, 1999;
W00040261A2, July 13, 2000; W09603144A1, February 8, 1996; EP1181314A1, February 27, 2002; W00123577A3, April 5; US6074817, June 13, 2000; US5965381, October 12, 1999;
W09741440A1, November 6, 1997; US6130066, October 10, 2000; US6004777, December 21, 1999; US5990091, November 23, 1999; W09840501A1, September 17, 1998;
W09840500A1, September 17, 1998; W00118035A2, March 15, 2001; W002068654A2, September 6, 2002;
W00189281A2, November 29, 2001; W00158478A, August 16, 2001; EP1118860A1, July 25, 2001; W00111040A1, February 15, 2001; W00073438A1, December 7, 2000;
W00071158A1, November 30, 2000; W00066727A1, November 9, 2000; W00052451A1, September 8, 2000;
W00052157A1, September 8, 2000; W00029008A2, May 25, 2000; W00006723A1, February 10, 2000. Additional disclosures, include Palmowski MJ, et al - J Immunol 2002;168(9):4391-8; Fang ZY, et al - Virology 2001;291(2):272-84; Firat H, et al - J Gene Med 2002;4(1):38-45; Smith SG, et al - Clin Cancer Res 2001;7(12):4253-61; Vonderheide RH, et al - Clin Cancer Res 2001;
7(11):3343-8; Firat H, et al - Eur 3 Iznmunol 2001;31(10):3064-74; Le T'T, et al - Vaccine 2001;19(32):4669-75; Fayolle C, et al - J Virol 2001;75(16):7330-8; Smith SG -Curr Opin Mol Ther 1999;1(1):10-5; Firat H, et al - Eur J Immunol 1999;29(10):3112-21; Mateo L, et al - 3 Immunol 1999;163(7):4058-63; Heemskerk MH, et al - Cell Immunol 1999;195(1):10-7;
Woodberry T, et al - J Virol 1999;73(7):5320-S; Hanke T, et al - Vaccine 1998;16(4):426-35;
Thomson SA, et al - J Immunol 1998;160(4):1717-23; Toes RE, et al - Proc Natl Acad Sci USA
1997;94(26):14660-5; Thomson SA, et al - J Immunol 1996;157(2):822-6; Thomson SA, et al -Proc Natl Acad Sci USA 1995;92(13):5845-9; Street MD, et al - Immunology 2002;106(4):526-36;
Hirano K, et al - Histochem Cell Biol 2002;117(1):41-53; Ward SM, et al -Virus Genes 2001;23(1):97-104; Liu WJ, et al - Virology 2000;273(2):374-82; Gariglio P, et al - Arch Med Res 1998;29(4):279-84; Suhrbier A - Immunol Cell Biol 1997;75(4):402-8; Fomsgaard A, et al -Vaccine 1999;18(7-8):681-91; An LL, et al - J Virol 1997;71(3):2292-302;
Whitton JL, et al - J
Virol 1993;67(1):348-52; Ripalti A, et al - J Clin Microbiol 1994;32(2):358-63; and Gilbert, S.C., et al., Nat. Biotech. 15:1280-1284, 1997.
[0073] One important feature that the disclosures in the preceding paragraph all share is their lack of appreciation for the desirability of regenerating housekeeping epitopes when the construct is expressed in a pAPC. This understanding was not apparent until the present invention.
Embodiments of the invention include sequences, that when processed by an immune proteasome, liberate or generate a housekeeping epitope. Embodiments of the invention also can liberate or generate such epitopes in immunogenically effective amounts. Accordingly, while the preceding references contain disclosures relating to polyepitope arrays, none is enabling of the technology necessary to provide or select a polyepitope capable of liberating a housekeeping epitope by action of an immunoproteasome in a pAPC. In contrast, embodiments of the instant invention are based upon a recognition of the desirability of achieving this result. Accordingly, embodiments of the instant invention include any nucleic acid construct that encodes a polypeptide containing at least one housekeeping epitope provided in a context that promotes its generation via immunoproteasomal activity, whether the housekeeping epitope is embedded in a string-of beads array or some other arrangement. Some embodiments of the invention include uses of one or more of the nucleic acid constructs or their products that are specifically disclosed in any one or more of the above-listed references. Such uses include, for example, screening a polyepitope for proper liberation context of a housekeeping epitope and/or an immune epitope, designing an effective immunogen capable of causing presentation of a housekeeping epitope and/or an immune epitope on a pAPC, immunizing a patient, and the like. Alternative embodiments include use of only a subset of such nucleic acid constructs or a single such construct, while specifically excluding one or more other such constructs, for any of the purposes disclosed herein. Some preferred embodiments employ these and/or other nucleic acid sequences encoding polyepitope arrays alone or in combination. For example, some embodiments exclude use of polyepitope arrays from one or more of the above-mentioned references. Other embodiments may exclude any combination or all of the polyepitope arrays from the above-mentioned references collectively.
Some embodiments include viral and/or bacterial vectors encoding polyepitope arrays, while other embodiments specifically exclude such vectors. Such vectors can encode carrier proteins that may have some immunostimulatory effect. Some embodiments include such vectors with such immunostimulatory/immunopotentiating effects, as opposed to immunogenic effects, while in other embodiments such vectors may be included. Further, in some instances viral and bacterial vectors encode the desired epitope as a part of substantially complete proteins which are not associated with the target cell. Such vectors and products are included in some embodiments, while excluded from others. Some embodiments relate to repeated administration of vectors. In some of those embodiments, nonviral and nonbacterial vectors are included. Likewise, some embodiments include arrays that contain extra amino acids between epitopes, for example anywhere from 1-6 amino acids, or more, in some embodiments, while other embodiments specifically exclude such arrays.
[0074) Embodiments of the present invention also include methods, uses, therapies, and compositions directed to various types of targets. Such targets can include, for example, neoplastic cells such as those listed below, for example; and cells infected with any virus, bacterium, protozoan, fungus, or other agents, examples of which are listed below, in Tables 1-5, or which are disclosed in any of the references listed above. Alternative embodiments include the use of only a subset of such neoplastic cells and infected cells listed below, in Tables 1-5, or in any of the references disclosed herein, or a single one of the neoplastic cells or infected cells, while specifically excluding one or more other such neoplastic cells or infected cells, for any of the purposes disclosed herein. The following are examples of neoplastic cells that can be targeted:
human sarcomas and carcinomas, e.g., fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilms' tumor, cervical cancer, testicular tumor, lung carcinoma, small cell lung carcinoma, bladder carcinoma, epithelial carcinoma, glioma, astrocytoma, medulloblastoma, craniopharyngioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, meningioma, melanoma, neuroblastoma, retinoblastoma; leukemias, e.g., acute lymphocytic leukemia and acute myelocytic leukemia (myeloblastic, promyelocytic, myelomonocytic, monocytic and erythroleukemia);
chronic leukemia (chronic myelocytic (granulocytic) leukemia and chronic lymphocytic leukemia);
and polycythemia vera, lymphoma (Hodgkin's disease and non Hodgkin's disease), multiple myeloma, Waldenstrom's macroglobulinemia, heavy chain disease, hepatocellular cancer, brain cancer, stomach cancer, liver cancer, and the like. Examples of infectious agents that infect the target cells can include the following: adenovirus, cytomegalovirus, Epstein-Barr virus, herpes simplex virus l, herpes simplex virus 2, human herpesvirus 6, varicella-zoster virus, hepatitis B virus, hepatitis D virus, papilloma virus, parvovirus B 19, polyomavirus BK, polyomavirus JC, hepatitis C virus, measles virus, rubella virus, human immunodeficiency virus (HIV), human T cell leukemia virus I, human T cell leukemia virus II, Chlamydia, Listeria, Salmonella, Legionella, Brucella, Coxiella, Rickettsia, Mycobacterium, Leishmania, Trypanasoma, Toxoplasma, Plasmodium, and the like.
Exemplary infectious agents and neoplastic cells are also included in Tables 1-5 below.
[0075] Furthermore the targets can include neoplastic cells described in or cells infected by agents that are described in any of the following references:
Jager, E. et al., "Granulocyte-macrophage-colony-stimulating factor enhances immune responses to melanoma-associated peptides in vivo," Int. J Cancer, 67:54-62 (1996); Kiindig, T.M., Althage, A., Hengartner, H. & Zinkernagel, R.M., "A skin test to assess CD8+ cytotoxic T
cell activity," Proc.
Natl. Acad Sci. USA, 89:7757-76 (1992); Bachmann, M.F. & Kundig, T.M., "In vitro vs. in vivo assays for the assessment of T- and B-cell function," Curr. Opin. Immunol., 6:320-326 (1994);
Kundig et al., "On the role of antigen in maintaining cytotoxic T cell memory," Proceedings of the National Academy of Sciences of the United States of America, 93:9716-23 (1996); Steinmann, R.M., "The dendritic cells system and its role in irnmunogenicity," Annual Review of Immunology 9:271-96 (1991); Inaba, K. et al., "Identification of proliferating dendritic cell precursors in mouse blood," Journal of Experimental Medicine, 175:1157-67 (1992); Young, J.W. &
Inaba, K., "Dendritic cells as adjuvants for class I major histocompatibility complex-restricted anti-tumor immunity," Journal of Experimental Medicine, 183:7-11 (1996); Kuby, Janis, Immunology, Second Edition, Chapter 15, W.H. Freeman and Company (1991); Austenst, E., Stahl, T., and de Gruyter, Walter, Insulin Pump Therapy, Chapter 3, Berlin, New York (1990);
Remington, The Science and Practice of Pharmacy, Nineteenth Edition, Chapters 86-88; Cleland, Jeffery L. and Langer, Robert (Editor), "Formulation and delivery of proteins and peptides,"
American Chemical Society (ACS Symposium Series, No. 567) (1994); Dickinson, Becton, which is fixed using Tegadenn transparent dressing TegadermTM 1624, 3M, St. Paul, MN 55144, USA;
Santus, Giancarlo and Baker, Richard, "Osmotic drug delivery: A review of the patent literature," Journal of Controlled Release, 35:1-21 (1995); Rammensee, U.S. Patent No. 5,747,269, issued May 05, 1998; Magruder, U.S. Patent No. 5,059,423, issued October 22, 1991; Sandbrook, U.S. Patent No.
4,552,651, issued November 25, 1985; Eckenhoff et al., U.S. Patent No.
3,987,790, issued October 26, 1976; Theeuwes, U.S. Patent No. 4,455,145, issued June 19, 1984; Roth et al. U.S. Patent No.
4,929,233, issued May 29 1990; van der Bruggen et al., U.S. Patent No.
5,554,506, issued September 10, 1996; Pfreundschuh, U.S. Patent No. 5,698,396, issued December 16, 1997;
Magruder, U.S. Patent No. 5,110,596, issued May 5, 1992; Eckenhoff, U.S.
Patent No. 4,619,652, issued October 28, 1986; Higuchi et al., U.S. Patent No. 3,995,631, issued December 07, 1976;
Maruyama, U.S. Patent No. 5,017,381, issued May 21, 1991; Eckenhoff, U.S.
Patent No.
4,963,141, issued October 16, 1990; van der Bruggen et al., U.S. Patent No.
5,558,995, issued September 24, 1996; Stolzenberg et al. U.S. Patent No. 3,604,417, issued September 14, 1971;
Wong et al., U.S. Patent No. 5,110,597, issued May 05, 1992; Eckenhoff, U.S.
Patent No.
4,753,651, issued June 28, 1988; Theeuwes, U.S. Patent No. 4,203,440, issued May 20, 1980;
Wong et al. U.S. Patent No. 5,023,088, issued June 11, 1991; Wong et al., U.S.
Patent No.
4,976,966, issued December 11, 1990; Van den Eynde et al., U.S. Patent No.
5,648,226, issued July 15, 199?; Baker et al., U.S. Patent No. 4,838,862, issued June 13, 1989;
Magruder, U.S.
Patent No. 5,135,523, issued August 04, 1992; Higuchi et al., U.S. Patent No.
3,732,865, issued May 15, 1975, ; Theeuwes, U.S. Patent No. 4,286,067, issued August, 25 1981;
Theeuwes et al., U.S. Patent No. 5,030,216, issued July 09, 1991; Boon et al., U.S. Patent No.
5,405,940, issued April 11, 1995; Faste, U.S. Patent No. 4,898,582, issued February 06, 1990;
Eckenhoff, U.S.
Patent No. 5,137,727, issued August 11, 1992; Higuchi et al., U.S. Patent No.
3,760,804, issued September 25, 1973; Eckenhoff et al., U.S. Patent No. 4,300,558, issued November 12, 1981;
Magruder et al., U.S. Patent No. 5,034,229, issued July 23, 1991; Boon et al., U.S. Patent No.
5,487,974, issued January 30, 1996; Kam et al., U.S. Patent No. 5,135,498, issued August 04, 1992; Magruder et al., U.S. Patent No. 5,174,999, issued December 29, 1992;
Higuchi, U.S.
Patent No. 3,760,805, September 25, 1973; Michaels, U.S. Patent No. 4,304,232, issued December 08, 1981; Magruder et al., U.S. Patent No. 5,037,420, issued October 15, 1991;
Wolfel et al., U.S.
Patent No. 5,530,096, issued June 25, 1996; Athadye et al., U.S. Patent No.
5,169,390, issued December 08, 1992; Balaban et al., U.S. Patent No. 5,209,746, issued May 11, 1993; Higuchi, U.S. Patent No. 3,929,132, issued December 30, 1975; Michaels, U.S. Patent No.
4,340,054, issued July 20, 1982; Magruder et al., U.S. Patent No. 5,057,318, issued October 15, 1991; Wolfel et al., U.S. Patent No. 5,519,117, issued May 21, 1996; Athadye et al., U.S.
Patent No. 5,257,987, issued November 02, 1993; Linkwitz et al., U.S. Patent No. 5,221,278, issued June 22, 1993;
Nakano et al., U.S. Patent No. 3,995,632, issued December 07, 1976; Michaels, U.S. Patent No.
4,367,741, issued January 11, 1983; Eckenhoff, U.S. Patent No. 4,865,598, issued September 12, 1989; Lethe et al., U.S. Patent No. 5,774,316, issued April 28, 1998;
Eckenhoff, U.S. Patent No.
4,340,048, issued July 20, 1982; Wong, U.S. Patent No. 5,223,265, issued June 29, 1993; Higuchi et al., U.S. Patent No. 4,034,756, issued July 12, 1977; Michaels, U.S. Patent No. 4,450,198, issued May 22, 1984; Eckenhoff et al., U.S. Patent No. 4,865,845, issued September 12, 1989;
Melief et. al., U.S. Patent No. 5,554,724, issued September 10, 1996;
Eckenhoff et al., U.S. Patent No. 4,474,575, issued October 02, 1984; Theeuwes, U.S. Patent No. 3,760,984, issued September 25, 1983; Eckenhoff, U.S. Patent No. 4,350,271, issued September 21, 1982;
Eckenhoff et al., U.S. Patent No. 4,855,141, issued August 08, 1989; Zingerman, U.S. Patent No.
4,872,873, issued October 10, 1989; Townsend et al., U.S. Patent No. 5,585,461, issued December 17, 1996;
Carulli, J.P. et al., J. Cellular Biochem Suppl., 30/31:286-96 (1998);
Tiireci, O., Sahin, U., and Pfreundschuh, M., "Serological analysis of human tumor antigens: molecular definition and implications," Molecular Medicine Today, 3:342 (1997); Rammensee et al., MHC
Ligands and Peptide Motifs, Landes Bioscience Austin, TX, 224-27, (1997); Parker et al., "Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains," J. Immunol. 152:163-175; Kido & Ohshita, Anal. Biochem., 230:41-47 (1995); Yamada et al., J. Biochem. (Tokyo), 95:1155-60 (1984); Kawashima et al., Kidney Int., 54:275-8 (1998);
Nakabayshi & Ikezawa, Biochem. Int. 16:1119-25 (1988); Kanaseki & Ohkuma, J.
Biochem.
(Tokyo), 110:541-7 (1991); Wattiaux et al., J. Cell Biol., 78:349-68 (1978);
Lisman et al., Biochem. J., 178:79-87 (1979); Dean, B., Arch. Biochem. Biophys., 227:154-63 (1983); Overdijk et al., Adv. Exp. Med. Biol., 101:601-10 (1978); Stromhaug et al., Biochem.
J., 335:217-24 (1998);
Escola et al., J. Biol. Chem., 271:27360-OS (1996); Hammond et al., Am. J.
Physiol., 267:F516-27 (1994); Williams & Smith, Arch. Biochem. Biophys., 305:298-306 (1993); Marsh, M., Methods Cell Biol., 31:319-34 (1989); Schmid & Mellman, Prog. Clin. Biol. Res., 270:35-49 (1988); Falk, K. et al., Nature, 351:290, (1991); Ausubel et al., Short Protocols in Molecular Biology, Third Edition, Unit 11.2 (1997); hypertext transfer protocol address 134.2.96.221/scripts/hlaserver.dll/EpPredict.htm; Levy, Morel, S. et al., Immunity 12:107-117 (2000); Seipelt et al., Virus Research, 62:159-68, 1999; Storkus et al., U.S.
Patent No. 5,989,565, issued November 23, 1999; Morton, U.S. Patent No. 5,993,828, issued November 30, 1999; Virus Research 62:159-168, (1999); Simard et al., U.S. Patent Application No.
10/026066, filed December 07, 2001; Simard et al., U.S. Patent Application No. 09/561571, filed April 28, 2000;
Simard et al., U.S. Patent Application No. 09/561572, filed April 28, 2000;
Miura et al., WO
99/01283, January 14, 1999; Simard et al., U.S. Patent Application No.
09/561074, filed April 28, 2000; Simard et al., U.S. Patent Application No. 10/225568, filed August 20, 2002; Simard et al., U.S. Patent Application No. 10/005905, filed November 07, 2001; Simard et al., U.S. Patent Application No. 09/561074, filed April 28, 2000.
[0076] Additional embodiments of the invention include methods, uses, therapies, and compositions relating to a particular antigen, whether the antigen is derived from, for example, a target cell or an infective agent, such as those mentioned above. Some preferred embodiments employ the antigens listed herein, in Tables 1-5, or in the list below, alone, as subsets, or in any combination. For example, some embodiments exclude use of one or more of those antigens.
Other embodiments may exclude any combination or all of those antigens.
Several examples of such antigens include MelanA (MART-I), gp100 (Pmel 17), tyrosinase, TRP-1, TRP-2, MAGE-1, MAGE-3, BAGS, GAGE-1, GAGE-2, CEA, RAGE, NY-ESO, SCP-1, Hom/Mel-40, PRAMS, p53, H-Ras, HER-2/neu, BCR-ABL, E2A-PRL, H4-RET, IGH-IGK, MYL-RAR, Epstein Ban virus antigens, EBNA, human papillomavirus (HPV) antigens E6 and E7, TSP-180, MAGE-4, MAGE-5, MAGE-6, p185erbB2, p180erbB-3, c-met, nm-23H1, PSA, TAG-72-4, CAM 17.1, NuMa, K-ras, (3-Catenin, CDK4, Mum-1, p16, as well as any of those set forth in the above mentioned references.
Other antigens are included in Tables 1-4 below.
[0077] Further embodiments include methods, uses, compositions, and therapies relating to epitopes, including, for example those epitopes listed in Tables 1-5. These epitopes can be useful to flank housekeeping epitopes in screening vectors, for example.
Some embodiments include one or more epitopes from Tables 1-5, while other embodiments specifically exclude one or more of such epitopes or combinations thereof.
Table 1 Virus Protein AA T cell epitope MHC molecule Position MHC ligand Anti en Adenovirus E3 9Kd 30-38 LIVIGILIL HLA-A*0201 SE . m N0.:44 Adenovirus EIA 234-243 SGPSNTPPEI H2-Db SE . )D N0.:45 Adenovirus E1B 192-200 VNIRNCCYI H2-Db (SE . ID N0.:46 Adenovirus EIA 234-243 SGPSNIPPEI T>I H2-Db SE . ID N0.:47 CSFV NS 2276-2284ENALLVALF SLA,haplotype of rotein d/d SE . ID N0.:48 Den a virusNS3 500-508 TPEGIIPTL HLA-B*3501 SE . ID N0.:49 EBV LMP-2 426-434 CLGGLLTMV HLA-A*0201 SE . ID N0.:50 EBV EBNA-1 480-484 NIAEGLRAL HLA-A*0201 SE .1D N0.:51 EBV EBNA-1 519-527 NLRRGTALA HLA-A*0201 SE . >D N0.:52 EBV EBNA-1 525-533 ALAIP CRL HLA-A*0201 SE .117 N0.:53 EBV EBNA-1 575-582 VLKDAIKDL HLA-A*0201 (SEQ. ID N0.:54) EBV EBNA-1 562-570 FMVFL THI HLA-A*0201 SE . m N0.:55 EBV EBNA-2 15-23 HLIVDTDSL HLA-A*0201 SE . B7 N0.:56 EBV EBNA-2 22-30 SLGNPSLSV HLA-A*0201 SE . ID N0.:57 EBV EBNA-2 126-134 PLASAMRML HLA-A*0201 SE . ID N0.:58) EBV EBNA-2 132-140 RMLWMANYI HLA-A*0201 SE . m N0.:59 EBV EBNA-2 133-141 MLWMANYN HL.A-A*0201 SE . ID N0.:60 EBV EBNA-2 151-159 ILPQGPQTA HLA-A*0201 SE . >D N0.:61 EBV EBNA-2 171-179 PLRPTAPTI HLA-A*0201 SE . ID N0.:62 EBV EBNA-2 205-213 PLPPATLTV HLA-A*0201 SE .1D N0.:63 EBV EBNA-2 246-254 RMHLPVLHV HLA-A*0201 SE . >D N0.:64 EBV EBNA-2 287-295 PMPLPPS L HLA-A*0201 (SEQ. ID N0.:65) EBV EBNA-2 294-302 LPPPAAPA HLA-A*0201 SE . ID N0.:66 EBV EBNA-2 381-389 SMPELSPVL HLA-A*0201 SE . ID N0.:67 EBV EBNA-2 453-461 DLDESWDYI HLA-A*0201 SE . ID N0.:68 EBV BZLFI 43-51 PLPCVLWPV HLA-A*0201 SE . ID N0.:69) EBV BZLFI 167-175 SLEECDSEL HLA-A*0201 SE . ID N0.:70 EBV BZLFl 176-t EIKRYKNRV HLA-A*OZOI
(SE . ID N0.:71) EBV BZLF1 195-203 QLL HYREV HLA-A*0201 (SE . ID N0.:72) EBV BZLFI 196-204 LL HYREVA HLA-A*0201 (SEQ. ID N0.:73 EBV BZLFI 217-225 LLK MCPSL HLA-A*0201 SE . 117 N0.:74 EBV BZLFI 229-237 SIIPRTPDV HLA-A*0201 SE . 117 N0.:75) EBV EBNA-6 284-293 LLDFVRFMGV HLA-A*0201 (SE . ID N0.:76 EBV EBNA-3 464-472 SVRDRLARL HLA-A*0203 SE . ID N0.:77 EBV EBNA-4 416-424 IVTDFSVIK HLA-A*1101 (SEQ. ID N0.:78 EBV EBNA-4 399-408 AVFDRKSDAK HLA-A*0201 (SE . B7 N0.:79 SE . ID N0.:80) SE . ID N0.:81) EBV EBNA-3 379-387 RPP1FIRRI. HLA-B7 SE . ID N0.:82 SEQ. ID N0.:83 SE . 117 N0.:84 SE . ID N0.:85 SE . ID N0.:86 EBV EBNA-1 72-80 R.P KRPSCI HLA-B7 SE . 117 N0.:87 SE . ID N0.:88) ( SEQ. ID N0.:89 SE . ID N0.:90 SE . ID N0.:91 SE . ID N0.:92 SE . ll~ N0.:93 SE . ID N0.:94 SE . ID N0.:9S
SE . ID N0.:96 (SE . ID N0.:97 SE . ID N0.:98 SE . 117 N0.:99 EBV LMP-2 236-244 RRRWRRLTV HLA-B*2704 SE . lD NO.:100 EBV EBNA-6 2S8-266 RRIYDLIEL HLA-B*2705 SE . ID NO.:101 EBV EBNA-3 4S8-466 YPLHE HGM HLA-B*3501 SEQ. )D NO.:102 EBV EBNA-3 4S8-466 YPLHE HGM HLA-B*3503 SEQ. ID NO.:103) SE . ID NO.:104 HCV env E 44-S1 ASRCWVAM HLA-B*3501 SE . 113 NO.: l OS
HCV core 27-3S G IVGGVYL HLA-B*40012 rotein SE . 117 N0.:106 HCV NSI 77-8S PPLTDFDQGW HLA-B*5301 SE . ID N0.:107 HCV core 18-27 LMGYIPLVGA H2-Dd rotein SEQ. ID NO.:108 HCV core 16-2S ADLMGYIPLV H2-Dd rotein SE . )D NO.:109 HCV NSS 409-424 MSYSWTGALVTPCAEE H2-Dd SE . ID NO.:110 HCV NS1 20S-213 KHPDATYSR Pa a-A06 SE . 117 NO.:111 HCV-1 NS3 400-409 KLVALGINAV HLA-A*0201 SEQ. ID NO.:112 HCV-1 NS3 440-448 GDFDSV~C Patr-B16 SE . )I7 N0.:113 HCV-1 env E 118-126 GNASRCWVA Patr-BI6 SE . ID NO.:114 HCV-1 NSI 1S9-167 TRPPLGNWF Patr-B13 SE . >D NO.:11 S
HCV-1 NS3 3S1-3S9 VPHPNIEEV Patr-B13 SE . ll~ NO.:116 HCV-1 ~~ NS3 438-446 YTGDFDSVI Patr-BO1 _ SE . ID N0.:117 HCV-1 NS4 328-335 SWAIKWEY Patr-All SEQ. ~ NO.:118 HCV-1 NSI 205-213 KHPDATYSR Patr-A04 SE . ID N0.:119 HCV-1 NS3 440-448 GDFDSVIDC Patr-A04 SEQ. ID N0.:120 SEQ. ID NO.:121 HIV a 24 267-275 IVGLNKNR HLA-A*3302 (SEQ. ID N0.:122) HIV a 24 262-270 EIYKRWIIL HLA-B8 (SEQ. ID NO.:123 HIV a 24 261-269 GEIYKRWII HLA-B8 SE . ID NO.:124 HIV a 17 93-101 EIKDTKEAL HLA-B8 SEQ. ID NO.:125 SEQ. ID N0.:126 HIV a 24 267-277 ILGLNKIVRMY HLA-B* 1501 (SEQ. ID N0.:127 SEQ. ILl N0.:128 HIV nef 115-125 YHTQGYFPQWQ HLA-B 17 SE . ID NO.:129 HIV nef 117-128 TQGYFPQWQNYT HLA-B17 SE . ID N0.:130 HIV I20 314-322 GRAFVT1GK HLA-B*2705 (SEQ. ID N0.:131 HIV a 24 263-271 KRWIII,GLN HLA-B*2702 SEQ. m NO.:132 HIV nef 72-82 VPLRPMTYK HLA-B*3501 SEQ. ID N0.:133 HIV nef 117-125 TQGYFP W HLA-B*3701 SE . ID NO.:134 HIV a 24 143-151 HQAISPRTI, HLA-Cw*0301 SEQ. ID NO.:135 HIV a 24 140-151 QMVH AISPRTL HLA-Cw*0301 SEQ, m N0.:136 HIV 120 431-440 MYAPPIGG I H2-Kd SE .117 N0.:137 HIV 160 318-327 RGPGRAFVTI H2-Dd SE . ll7 N0.:138 HIV 120 17-29 MPGRAFVTI H2-Ld SEQ. ID N0.:139 HIV-1 RT 476-484 LKEPVHGV HLA-A*0201 I
SE . ID N0.:140 HIV-1 nef 190-198 AFHHVAREL HLA-A*0201 SEQ. ID N0.:141 HIV-1 I60 120-128 KLTPLCVTL HLA-A*0201 SE . ID NO.:142 HIV-1 60 814-823 SLLNATDIAV HLA-A*0201 SE . ID NO.:143) HIV-1 RT 179-187 MY YMDDL HLA-A*0201 SE . 117 N0.:144 HIV-1 a 17 77-85 SLYNTVATL HLA-A*0201 SE . ID NO.:145) HIV-1 160 315-329 RGPGRAFVT1 HLA-A*0201 SE . ID NO.:146) SE .117 N0.:147 HIV-1 nef 73-82 VPLRPMTYK HLA-A3 SE . 117 NO.:148) SE . ID N0.:149) HIV-1 a 17 20-29 RLRPGGKKK HLA-A3 SE . ID NO.:150 SE . ID NO.:151 HIV-1 nef 74-82 VPLRPMTYK HLA-a* 11 SE . ID N0.:152 HIV-1 a 24 325-333 AIF SSMTK HLA-A*1101 SE . 117 NO.:153 HIV-1 nef 73-82 VPLRPMTYK HLA-A* 1101 SEQ. ID NO.:154 HIV-1 nef 83-94 AAVDLSHFLKEK HLA-A*1101 SE . ID NO.:155 HIV-1 a 24 349-359 AC GVGGPGGHK HLA-A*1101 SEQ. ID N0.:156 HIV-1 a 24 203-212 ETINEEAAEW HLA-A25 SE . ID N0.:157 HIV-1 nef 128-137 TPGPGVRYPL HLA-B7 SE . ID N0.:158 HIV-1 a 17 24-31 GGKKKYKL HLA-B8 SE . ID N0.:159 SEQ. ID NO.:160 HIV-1 a 24 298-306 DRFYKTLRA HLA-B 14 SE . II7 N0.:161 SE . ID NO.:162 HIV-1 a 24 265-24 KRWIII,GLNK HLA-B*2705 SEQ. ID NO.:163 HIV-1 nef 190-198 AFHHVAREL HLA-B*5201 SE . ll~ NO.:164 SE . 117 NO.:165 EBV EBNA-6 130-139 EENLLDFVRF HLA-B*4403 SE . ID NO.:166 _ I - ~ - - (SEQ. ID NO.:167) SE . m N0.:168 SE . >D N0.:169 HBV sA 348-357 GLSPTVWLSV HLA-A*0201 SE . ID NO.:170 HBV SA 335-343 WLSLLVPFV HLA-A*0201 SE . )D NO.:171 HBV cA 18-27 FLPSDFFPSV HLA-A*0201 SEQ. ID N0.:172) HBV cA 18-27 FLPSDFFPSV HLA-A*0202 SE . ID NO.:173 HBV cA 18-27 FLPSDFFPSV HLA-A*0205 SE . ID NO.:174 HBV cA 18-27 FLPSDFFPSV HLA-A*0206 SE . ID N0.:175) HBV of 575-583 FLLSLGIHL HLA-A*0201 SE . ID NO.:176 HBV of 816-824 SLYADSPSV HLA-A*0201 SE . ID NO.:177 HBV of 455-463 GLSRYVARL HLA-A*0201 SE . ID NO.:178 HBV env 338-347 LLVPFV WFV HLA-A*0201 SEQ. ID NO.:179) HBV of 642-650 ALMPLYACI HLA-A*0201 SEQ. ID NO.:180 HBV env 378-387 LLPIFFCLWV HLA-A*0201 SE . )D N0.:181 HBV of 538-546 YMDDVVLGA HLA-A*0201 SE . B7 NO.:182 HBV env 250-258 LLLCLIFLL HLA-A*0201 SEQ. ID N0.:183 HBV env 260-269 LLDYQGMLPV HLA-A*0201 SE . ID NO.:184 HBV env 370-379 SNSPFIPLL HLA-A*0201 SE . ID N0.:185 HBV env 183-191 FLLTRILTI HLA-A*0201 SE . ID NO.:186 HBV cA 88-96 YVNVNMGLK HLA-A* 1101 SEQ. ID N0.:187 HBV cA 141-151 STLPETTVVRR HLA-A*3101 SEQ. ID N0.:188 HBV eA 141-151 STLPETTVVRR HLA-A*6801 SE . ID N0.:189 HBV cA 18-27 FLPSDFFPSV HLA-A*6801 SE . ID NO.:190 HBV sA 28-39 IP SLDSWWTSL H2-Ld SEQ. )D NO.:191 HBV cA 93-100 MGLKFR L H2-Kb SE .117 NO.:l92 ~V ~ preS ~ 141-149~ STBXQSGXQ ~ HLA-A*0201 SE . ID N_O.:193 HCMV B 618-628 FIAGNSAYEYV HLA-A*0201 SE . ID N0.:194 SE . ID NO.:195 HCMV 65 397-411 DDVWTSGSDSDEELV HLA-b35 SE . ID NO.: I
HCMV 65 123-131 IPSINVHHY HLA-B*3501 SE . ID NO.:197) HCMV 65 495-504 NLVPMVATVO HLA-A*0201 SE . ID N0.:198 SE . ID NO.:199 HCV MP 17-25 DLMGYIPLV HLA-A*0201 SE . ID N0.:200 HCV MP 63-72 LLALLSCLTV HLA-A*0201 SEQ. ID N0.:201 HCV MP 105-112 ILHTPGCV HLA-A*0201 SE . ID N0.:202 HCV env E 66-75 LRRHIDLLV HLA-A*0201 SE . 117 N0.:203 HCV env E 88-96 DLCGSVFLV HLA-A*0201 SE . ID N0.:204 HCV env E 172-180 SMVGNWAKV HLA-A*0201 SEQ. ID N0.:205 HCV NSI 308-316 HLII NNDV HLA-A*0201 SE . ID N0.:206) HCV NSI 340-348 FLLLADARV HLA-A*0201 SEQ. ID N0.:207 HCV NS2 234-246 GLRDLAVAVEPVV HLA-A*0201 SE .11? N0.:208 HCV NSI 18-28 SLLAPGAKQNV HLA-A*0201 SE . D7 N0.:209 HCV NSI 19-28 LLAPGAK NV HLA-A*0201 SEQ. ID N0.:210 HCV NS4 192-201 LLFNILGGWV HLA-A*0201 SE . ID N0.:211 HCV NS3 579-587 YLVAY ATV HLA-A*0201 SE . ID N0.:212 HCV core 34-43 YLLPRRGPRL HLA-A*0201 rotein SE . ID N0.:213 HCV MP 63-72 LLALLSCLTI HLA-A*0201 SE . ID N0.:214) HCV NS4 174-182 SLMAFTAAV HLA-A*0201 SEQ. ID N0.:21 S
HCV NS3 67-75 CINGVCWTV HLA-A*0201 SE . ID N0.:216 HCV NS3 163-171 LLCPAGHAV HLA-A*0201 SE . ID N0.:217 HCV NS5 239-247 IL,DSFDPLV HLA-A*0201 SE .117 N0.:218 HCV NS4A 236-244 ILAGYGAGV HLA-A*0201 SE . ID N0.:219) HCV NSS 714-722 GL DCTMLV HLA-A*0201 (SE . ID N0.:220 HCV NS3 281-290 TGAPVTYSTY HLA-A*0201 SEQ. ID N0.:221 HCV NS4A 149-157 HMWNFISGI HLA-A*0201 SE . B7 N0.:222 HCV NSS 575-583 RVCEKMALY HLA-A*0201-A3 (SEQ. ID N0.:223) HCV NS1 238-246 TINYTIFK HLA-A*1101 SEQ. ID N0.:224) SEQ. ID N0.:225 HCV core 40-48 GPRLGVRAT HLA-B7 rotein SE .117 N0.:226 HIV-1 120 380-388 SFNCGGEFF HLA-Cw*0401 (SEQ. ID N0.:227 HIV-1 RT 206-214 TEMEKEGKI H2-Kk SE . ID N0.:228) HIV-1 17 18-26 KIRLRPGGK HLA-A*0301 SEQ. ID N0.:229 HIV-1 P17 20-29 RLRPGGKKKY HLA-A*0301 (SEQ. ID N0.:230 HIV- I RT 325-333 AIFQSSMTK HLA-A*0301 SE . ID N0.:231) SE . ID N0.:232 HIV-1 RT 508-517 IYQEPFKNLK HLA-All (SEQ. ID N0.:233 (SEQ. ID N0.:234) SEQ. ID N0.:235) HN-1 a 24 145-155 QAISPRTLNAW HLA-A25 SE . ID N0.:236 HN-1 a 24 167-175 EVIPMFSAL HLA-A26 SEQ. >I7 N0.:237 (SEQ. ID N0.:238 SEQ. ID N0.:239) SEQ. ID N0.:240 (SEQ. ID N0.:241 HIV-1 RT 71-79 ITLWQRPLV HLA-A*6802 SE . ID N0.:242 HIV-1 RT 85-93 DTVLEEMNL HLA-A*6802 SEQ.117 N0.:243 HIV-1 RT 71-79 ITLW RPLV HLA-A*7401 SE .1T7 N0.:244 HIV-1 a 24 148-156 SPRTLNAWV HLA-B7 SE . a? N0.:245 HIV-1 a 24 179-187 ATP DLNTM HLA-B7 SE .1D N0.:246 SE . >D N0.:247 HIV-1 41 ~ 843-8S1 IPRRIRQGL HLA-B7 SE . ~ N0.:248 SE . m N0.:249 HIV-1 nef 13-20 WPTVRERM HLA-B8 SE . ID N0.:2S0 HIV-1 nef 90-97 FLKEKGGL HLA-B8 SE . ID N0.:2S 1 ~-1 a 24 183-191 DLNTMLNTV HLA-B14 SE . B7 N0.:252 SE . ID N0.:253 SE .1D N0.:254 SE . ID N0.:255 HN-1 nef 73-82 VPLRPMTYK HLA-B27 SE . m N0.:2Sb SE . ID N0.:2S7 HIV-1 nef 105-114 RR DILDLWI HLA-B*2705 SE . ~ N0.:2S8) HIV-1 nef 134-141 RYPLTFGW HLA-B*2705 SEQ. ID N0.:2S9 SEQ. m N0.:260 SE . lZ7 N0.:261 ~-1 120 42-S2 VPVWKEATTTL HLA-B3S
SE . m N0.:262 SE . ID N0.:263 HIV-1 a 24 2S4-262 PPIPVGDIY HLA-B35 SE , m N0.:264 SE . ~ N0.:265) SE . ID N0.:266 HIV-1 a 2 45-253 NPVPVGNIY HLA-B3S
SE . ll~ N0.:267 ~-1 n ef 1 20-128 FPDWQNYT HLA-B37 Y
SE . ID N0.:268 HIV-1 a 24 1 93-201 H AAM ML HLA-B42 G
SE . m N0.:269 WO 2003/063770 PCT/US2002/036(19R
SE . ID N0.:270) SE . ID N0.:271 SE . ID N0.:272) _ HN-1 a 24 325-333 NANPDCKTI HLA-BS I
SE . ID N0.:273 HN-1 a 24 275-282 RMYSPTSI HLA-BS2 SEQ. ID N0.:274) HN-I 120 42-S1 VPVWKEATTT HLA-B*5501 SE . ID N0.:275) HN-I a 24 147-1SS ISPRTLNAW HLA-B57 (SE . ID N0.:276 HN-1 a 24 240-249 TSTL E IGW HLA-BS7 (SE .117 N0.:277) HIV-I a 24 162-172 KAFSPEVIPMF HLA-BS7 SE . ID N0.:278 HIV-1 a 24 311-319 ASQEVKNW HLA-BS7 SE . ID N0.:279 HIV-1 a 24 311-319 QAS DVKNW HLA-B57 SEQ. ID N0.:280 HN-1 nef 116-12S HT GYFPDW HLA-BS7 SEQ. ID N0.:281) HIV-1 nef 120-128 YFPDWQNYT HLA-BS7 (SE .117 N0.:282 HIV-1 a 24 240-249 TSTLQEQIGW HLA-BS8 SE . ID N0.:283) SE . ID N0.:284 SEQ. m N0.:285 (SEQ. m N0.:286 SE .117 N0.:287) HN-1 nef 117-127 TQGYFPDW NY HLA-B62 SE .117 N0.:288) HIV-1 nef 84-91 AVDLSHFL HLA-B62 SEQ. >I? N0.:289 HIV-1 a 24 168-175 VIPMFSAL H LA-Cw*0102 ( SEQ. m N0.:290 F
SE . ll7 N0.:291 HN-1 120 3?S-383 FNCGGEFF H LA-B1S
S
SE . m N0.:292 HIV-1 n ef 1 36-14S LTFGWCYKL H LA-A*0201 P
SE . ID N0.:293 HIV-1 n ef 1 80-189 LEWRFDSRL H LA-A*0201 V
SE . ID N0.:294 HN-1 n ef 6 8-77 PVTP VPLR H LA-B7 F
WO 2003/063770 PCT/US2002/036098. .____, I SEQ. ID N0.:295 HIV-1 nef 128-137 TPGPGVRYPL HLA-B7 ~SEQ. ID N0.:296) HIV-1 a 24 308-316 AS EVKNW HLA-Cw*0401 SE . ID N0.:297 HIV-lIIIB RT 273-282 VPLDEDFRKY HLA-B35 SE . ID N0.:298 HIV-l IIIB RT 25-33 NPDIVIY Y HLA-B35 SE . ID N0.:299 HIV-l IIIB 41 557-565 RAIEA AHL HLA-B51 SE . >D N0.:300) HIV-lIIIB RT 231-238 TAFTIPSI HLA-B51 SE . >I? NO.:301 HIV- I IIIB 24 215-223 VHPVHAGPIA HLA-B*5501 SE . ID N0.:302 HN-IIIIB 120 156-165 NCSFNISTSI HLA-Cw8 SE . ID N0.:303 HN- I IIIB 120 241-249 CTNVSTV C HLA-Cw8 SE . >I7 N0.:304 HIV-15F2 120 312-320 IGPGRAFHT H2-Dd SEQ. ID N0.:305 HIV-15F2 0l 25-33 NPDIVIY Y HLA-B*3501 SEQ. >D N0.:306 HIV-15F2 0l 432-441 EPIVGAETFY HLA-B*3501 SE . >D N0.:307 HIV-15F2 0l 432-440 EPNGAETF HLA-B*3501 SE . ID N0.:308 HIV-15F2 0l 6-14 SPAIFQSSM HLA-B*3501 SEQ. ID N0.:309 HIV-15F2 0l 59-68 VPLDKDFRKY HLA-B*3501 (SEQ. II? N0.:310 HIV-15F2 0l 6-14 IPLTEEAEL HLA-B*3501 SEQ. )D N0.:311 HIV-15F2 nef 69-79 RP VPLRPMTY HLA-B*3501 SEQ. m N0.:312 HIV-1 SF2 nef 66-74 FPVRP VPL HLA-B*3501 SE . m N0.:313 HIV-15F2 env 10-18 DPNPQEVVL HLA-B*3501 SEQ. ID N0.:314 HIV-1 SF2 env 7-15 RPIVSTQLL HLA-B*3501 SEQ. >D N0.:315 HIV-15F2 0l 6-14 IPLTEEAEL HLA-B51 SE . >D N0.:316 HN-15F2 env 10-18 DPNPQEVVL HLA-B51 SEQ. ID N0.:317 HIV-1 SF2 a 24 199-207 AMQMLKETI H2-Kd SEQ. >D N0.:318 HN-2 a 24 182-190 TPYDrNQML HLA-B*5301 SE .1D N0.:319 HN-2 a 260-269 RRWI LGL KV HLA-B*2703 SEQ.1D N0.:320 SE . ID N0.:321 SE . 117 N0.:322 HPV 6b E7 21-30 GLHCYE LV HLA-A*0201 SE . ID N0.:323 HPV 6b E7 47-55 PLK HF IV HLA-A*0201 SE . ID N0.:324 HPV 11 E7 4-12 RLVTLKDIV HLA-A*0201 SE . ID N0.:325 HPV 16 E7 86-94 TLGIVCPIC HLA-A*0201 SE .117 N0.:326 HPV 16 E7 85-93 GTLGIVCPI HLA-A*0201 SE . >D N0.:327 HPV 16 E7 12-20 MLDL PETT HLA-A*0201 SE . ID N0.:328 HPV16 E7 11-20 YMLDL PETT HLA-A*0201 SE . ID N0.:329 HPVl6 E6 15-22 RPRKLPQL HLA-B7 SE . ID N0.:330 HPV 16 E6 49-57 RAHYNIVTF HW-Db SE . ID N0.:331 HSV B 498-505 SSIEFARL H2-Kb SE . 117 N0.:332 HSV-1 C 480-488 GIGIGVLAA HLA-A*0201 SEQ. ID N0.:333 HSV-1 ICP27 448-456 DYATLGVGV H2-Kd SEQ. ID N0.:334) Virus Protein T cell epitope MHC molecule MHC ligand Anti en HSV-1 ICP27 322-332 LYRTFAGNPRA H2-Kd SEQ. ID N0.:335 HSV-1 UL39 822-829 TFDFGRL H2-Kb SE . ID N0.:336 HSV-2 C 446-454 GAGIGVAVL HLA-A*0201 SE . ID N0.:337) HLTV-1 TAX 11-19 LLFGYPVYV HLA-A*0201 SE . ID N0.:338 Influenza MP 58-66 GILGFVFTL HLA-A*0201 SEQ.117 N0.:339 Influenza MP 59-68 ILGFVFTLTV HLA-A*0201 SEQ. ID N0.:340) Influenza NP 265-273 ILRGSVAHK HLA-A3 SE . ID N0.:341 Influenza NP 91-99 KTGGPIYKR HLA-A*6801 SE .117 N0.:342 Influenza NP 380-388 ELRSRYWAI HLA-B8 SE . ID N0.:343) Influenza NP 381-388 LRSRYWAI HLA-B*2702 SE . D7 N0.:344 Influenza NP 339-347 EDLRVLSFI HLA-B*3701 SE .117 N0.:345 Influenza NSI 158-166 GEISPLPSL HLA-B44 SEQ. ID N0.:346 Influenza NP 338-346 FEDLRVLSF HLA-B44 SE . ID N0.:347 Influenza NSI 158-166 GEISPLPSL HLA-B*4402 SE . ID N0.:348 Influenza NP 338-346 FEDLRVLSF HLA-B*4402 SEQ.117 N0.:349 Influenza PBI 591-599 VSDGGPKLY . HLA-Al SE . ID N0.:350 Influenza NP 44-52 CTELKLSDY HLA-Al A
SE . ID N0.:351 Influenza NSI 122-130 AIMDKNIIL HLA-A*0201 SE . ID N0.:352 Influenza NSI 123-132 IMDKNIILKA HLA-A*0201 A
SE . ID N0.:353 Influenza NP 383-391 SRYWAIRTR HLA-B*2705 A
SEQ. ID N0.:354 Influenza NP 147-155 TY RTRALV H2-Kd A
SEQ. ID N0.:355 Influenza HA 210-219 TYVSVSTSTL H2-Kd A
SE . ID N0.:356 Influenza HA 518-526 IYSTVASSL H2-Kd A
SE . ID N0.:357 Influenza HA 259-266 FEANGNLI H2-Kk A
SEQ. ID N0.:358 Influenza HA 10-18 IEGGWTGMI H2-Kk A
SE . ID N0.:359) Influenza NP 50-57 SDYEGRLI H2-Kk A
(SEQ. ID N0.:360) Influenza NSI 152-160 EEGAIVGEI H2-Kk a SEQ. LD N0.:361 Influenza NP 336-374 ASNENMETM H2Db SE .117 N0.:362 Influenza NP 366-374 ASNENMDAM H2Db SEQ. ID N0.:363 Influenza NP 85-94 KLGEFYN MM HLA-A*0201 B
SEQ. ID N0.:364 Influenza NP 85-94 KAGEFYNQMM HLA-A*0201 B
SEQ. ID N0.:365 Influenza HA 204-212 LYQNVGTYV H2Kd JAP
SE . ID N0.:366 Influenza HA 210-219 TYVSVGTSTL H2-Kd JAP
(SEQ. ID N0.:367 Influenza HA 523-531 VYQILATYA H2-Kd JAP
SE . ID N0.:368 Influenza HA 529-537 IYATVAGSL H2-Kd JAP
SE . ID N0.:369 Influenza HA 210-219 TYVSVGTSTI L>I H2-Kd JAP
SE . ID N0.:370 Influenza HA . 255-262 FESTGNLI H2-Kk JAP
SE . ID N0.:371 JHMV cA 318-326 APTAGAFFF H2-Ld SE . ID N0.:372 LCMV NP 118-126 RP ASGVYM H2-Ld SE .117 N0.:373 LCMV NP 396-404 F P NGQFI H2-Db SEQ. ID N0.:374 LCMV GP 276-286 SGVENPGGYCL H2-Db (SEQ. ID N0.:375 LCMV GP 33-42 KAVYNFATCG H2-Db (SEQ. ID N0.:376 MCMV 89 168-176 YPHFMPTNL H2-Ld SE . >D N0.:377 MHV spike 510-518 CLSWNGPHL H2-Db rotein SE . ID N0.:378 MMTV env 36 474-482 SFAVATTAL H2-Kd SEQ. D7 N0.:379 MMTV a 27 425-433 SYETFISRL H2-Kd SE . ID N0.:380 MMTV env 73 544-551 ANYDFICV H2-Kb (SEQ. ID N0.:381 MuLV env 15E 574-581 KSPWFTTL H2-Kb SEQ. ID N0.:382 MuLV env gp70189-196 SSWDFITV H2-Kb SE . ID N0.:383 MuLV a 75K 75-83 CCLCLTVFL H2-Db (SE .117 N0.:384 MuLV env 70 423-431 SPSYVYHQF H2Ld SE . ID N0.:385 MV F rotein437-447 SRRYPDAVYLH HLA-B*2705 (SEQ. ID N0.:386 My F rotein438-446 RRYPDAVYL HLA-B*2705 Virus Protein AA T cell epitope MHC MHC molecule Position ligand Anti en (SE . ID N0.:387 My NP 281-289 YPALGLHEF H2-Ld (SE . ID N0.:388 My HA 343-351 DPV117RLYL H2-Ld SE . ID N0.:389 MV HA 544-552 SPGRSFSYF H2-Ld (SEQ. ID N0.:390 Poliovirus VP1 111-118 TYKDTV L H2-kd SE . ID N0.:391 Poliovirus VP1 208-217 FYDGFSKVPL H2-Kd SE . ID N0.:392 Pseudorabies6111 455-463 IAGIGILAI HLA-A*0201 virus SE . ID N0.:393 RabiesvirusNS 197-205 VEAEIAHQI H2-Kk SEQ. ID N0.:394 Rotavirus VP7 33-40 11YRFLL1 H2-Kb SE . ID N0.:395) Rotavirus VP6 376-384 VGPVFPPGM H2-Kb SE . ID N0.:396 Rotavirus VP3 585-593 YSGYIFRDL H2-Kb SE .117 N0.:397 RSV M2 82-90 SYIGSINNI H2-Kd SEQ. ID N0.:398 SN a 11 C 179-190 EGCTPYDTNQML Mamu-A*O1 SE . )17 N0.:399 SV NP 324-332 FAPGNYPAL H2-Db SEQ. ID N0.:400 SV NP 324-332 FAPCTNYPAL H2-Kb SE . ID N0.:401 SV40 T 404-411 VVYDFLKC H2-Kb SE . ID N0.:402) SV40 T 206-215 SAINNYA KL H2-Db SE . ID N0.:403 SV40 T 223-231 CKGVNKEYL H2-Db SE . ID N0.:404 SV40 T 489-497 GINNLDNL H2-Db SEQ. ID N0.:405 SV40 T 492-S00 NNLDNLRDY(L) H2-Db SEQ. ID N0.:406 SV40 T 560-568 SEFLLEKRI H2-Kk SEQ. ID N0.:407 VSV NP 52-59 RGYVY GL H2-Kb SEQ. ID N0.:408 Table 2 IEILA-A1 Position Anti en Source T cell a EADPTGHSY MAGE-1 161-169 ito es SEQ. ID N0.:409 VSDGGPNLY Influenza A PB 1591-599 SEQ. ID N0.:410 CTELKLSDY Influenza A NP 44-52 SEQ. ID N0.:411 SEQ. ff~ N0.:412 HLA-A201 MLLSVPLLLG Calreticulin si al se uence SEQ, )D N0.:413 SE . >D N0.:414 YMDGTMS V Tyrosinase 369-377 SE . ID N0.:415 SEQ. ID N0.:416 LLGFVFTLTV Influenza MP 59-68 SEQ. ID N0.:417 LLFGYPVYVV HTLV-1 tax 11-19 (SEQ. )D N0.:418 GLSPTVWLSV HBV sA 348-357 SEQ.117 N0.:419 WLSLLVPFV HBV sA 335-343 SE . ID N0.:420 FLPSDFFPSV HBV cA 18-27 SEQ. ID N0.:421) SEQ. ID N0.:422) (SEQ. )D N0.:423 KLGEFYNQMM Influenza BNP 85-94 SEQ. m N0.:424) SE . ID N0.:425) SE . ID N0.:426) (SE . )D N0.:427 MLLAVLYCL T rosinase 1-9 SE . II7 N0.:428) AAGIGILTV Melan A~IVIart-127-35 (SEQ. ID N0.:429 YLEPGPVTA Pmel 17/ 100 480-488 SEQ. ID N0.:430 ~ ILDGTATLRL Pmel 17/ gp 100 457-466 SE . ID N0.:431) LLDGTATLRL Pmel 100 457-466 SE . ID N0.:432 ITD VPFSV Pmel 100 209-217 SE . ID N0.:433 KTWGQYWQV Pmel 100 154-162 SE . ID N0.:434) TITDQVPFSV Pmel 100 208-217 SE . ID N0.:435) AFHIIVAREL HIV- I nef 190-198 SE . ID N0.:436) YLNKIQNSL P. falci arum CSP 334-342 SE . ID N0.:437 MMRKLAILSV P. falci arum CSP 1 -10 SE . ID N0.:438 KAGEFYN MM Influenza BNP 85-94 SE . ID N0.:439) SEQ. ID N0.:440) SE . ID N0.:441 SE . ID N0.:442) SE . ID N0.:443 SE . ID N0.:444) SEQ. ID N0.:445) SE . ID N0.:446) SE . ID N0.:447 SE . ID N0.:448 SE . ID N0.:449) SEQ. >D N0.:450 SE .117 N0.:451 SEQ.117 N0.:452) SE . ID N0.:453 SE . ID N0.:454 SE . ID N0.:455 SE . ID N0.:456 SE . ID N0.:457 SE . ID N0.:458 SEQ, ID N0.:459 SE . ID N0.:460 SE . ID N0.:461 SE . ID N0.:462 SE . ID N0.:463 SE . ID N0.:464 AIMDKNIIL Influenza A NS1 122-130 SE . ID N0.:465 IMDKNIILKA Influenza A NSl 123-132 SE . ID N0.:466 SE . ID N0.:467 SE . ID N0.:468 LRRHIDLLV HCV env E 66-75 SEQ, ID N0.:469 DLCGSVFLV HCV env E 88-96 SEQ. ID N0.:470 SMVGNWAKV HCV env E 172-180 SE . ID N0.:471 SE . ID N0.:472 SEQ. ID N0.:473 SEQ. ID N0.:474 SE .117 N0.:475 LLAPGAK NV HCV NSl 19-28 SE . ID N0.:476 SE . ID N0.:477 SE .117 N0.:478 SEQ. >D N0.:479 SE . 117 N0.:480 SE . >D N0.:481 (SE . ID N0.:482 SE . ID N0.:483 VLYRYGSFSV Pmel 100 476-485 SE . >D N0.:484 YIGEVLVSV Non-filament forming class I myosin family (HA-2)**
(SE . ID N0.:485 SE . ID N0.:486 LLVPFV WFW HBV env 338-347 SE . ID N0.:487 SE . ID N0.:488 (SE . ID N0.:489 (SEQ. )D N0.:490 YLLPRRGPRL HCV core rotein 34-43 SE . ID N0.:491 LLPIFFCLWV HBV env 378-387 SE . ID N0.:492 YMDDVVLGA HBV Pol 538-546 SE . ID N0.:493 SE . ID N0.:494 (SEQ. ID N0.:495 SE . ID N0.:496 SE . ID N0.:497 SE . )D N0.:498 VMNILL YVV Glutarnic acid decarbox lase 114-123 SE . >D N0.:499 ILTVILGVL Melan A/Mart- 32-40 SE . ID NO.:500 SE . >D NO.:501 SE . ID N0.:502 IL,DSFDPLV HCV NSS 239-247 SE . ID N0.:503 LLLCLIFLL HBV env 250-258 (SEQ. m N0.:504 LIDYQGMLPV HBV env 260-269 SEQ. ID N0.:505 SIVSPFIPLL HBV env 370-379 SE . ID N0.:506 FLLTRILTI HBV env 183-191 (SE . ID N0.:507 HLGNVKYLV P. faci arum TRAP 3-11 SE . ID N0.:508 GIAGGLALL P. faci arum TRAP 500-508 SE . ID N0.:509 SEQ.117 N0.:510 SE .117 N0.:511 (SEQ. ID N0.:512 SEQ. ID N0.:513) VLPDVFIRCV N-acetylglucosaminyltransferase V
Gnt-V intron SEQ. ID N0.:514 VLPDVFIRC N-acetylglucosaminyltransferase V
Gnt-V intron SEQ. ID N0.:515 AVGIGIAVV Human CD9 SEQ. ID N0.:516 LVVLGLLAV Human lutam ltransferase SE . ID N0.:517 ALGLGLLPV Human G rotein cou led rece for (SEQ. ID N0.:518) SEQ. ID N0.:519 SE .117 N0.:520 IAGIGILAI Pseudorabies GIN 455-463 SEQ.117 N0.:521 LIVIGILIL Adenovirus 3 E3 9kD 30-38 SEQ. ID N0.:522 LAGIGLIAA S. Lincolnensis ImrA
SE . ID N0.:523 VDGIGILTI Yeast sa-177-85 SEQ. ID N0.:524 GAGIGVLTA B. polymyxa, [3cndoxylanase (SEQ. ll7 N0.:525) AAGIGII I E. coli methionine s thane SEQ. ID N0.:526 AGIGILLA E. coli h othetical rotein SEQ. ID N0.:527 KARDPHSGHFV CDK4wl 22.32 SEQ. ID N0.:528 SEQ. ID N0.:529 SEQ. ID N0.:530 SLYNTVATL HIV- I a 17 77-85 SEQ. ID N0.:531 ELVSEFSRV HER-2, m>V substituted SE . ID N0.:532 SEQ. ID N0.:533 SEQ. ID N0.:534 SEQ. ID N0.:535 GLHCYEQLV HPV 6b E7 21-30 SEQ. ID N0.:536 PLKQHFQIV HPV 6b E7 47-55 SE . ID N0.:537 SE . >I7 N0.:538 AIMEKNIML Influenza Alaska NS 1 122-130 SEQ. ID N0.:539 YLKTI NSL P. falci arum c 36 CSP
SEQ. ID N0.:540 YLNKIQNSL P. falci arum c 39 CSP
SEQ. ID N0.:541 YMLDL PETT HPV 16 E7 11-20*
SE .117 N0.:542 LLMGTLGIV HPV16 E7 82-90**
SE . ID N0.:543 SEQ. ID N0.:544 SE . ID N0.:545 SEQ. ID N0.:546 TIH>DIIL,EC HPV 16 E6 29-37 SEQ. ID N0.:547 SE . ID N0.:548) VIL,GVLLLI Melan A/Mart-1 35-43 SE . ID N0.:549 ALMDKSLHV Melan A/Mart- 1 56-64 SE . ID N0.:550 GIL,TVILGV Melan A/Mart- 1 31-39 SE . ID NO.:551 T cell a ito MINAYLDKL P. Falci arum STARP 523-531 es SE . ID N0.:552) AAGIGILTV Melan A/Mart- 127-35 SE . ID N0.:553 FLPSDFFPSV HBV cA 18-27 SE . ID N0.:554 Motif unknownSVRDRLARL EBNA-3 464-472 T cell a ito SE . ID NO.:555 es T cell a ito AAGIGILTV Melan A/Mart-1 27-35 es SE . ID N0.:556 FAYDGKDYI Human MHC I-of 140-148 SE . )D N0.:557 T cell a ito AAGIGILTV Melan A/Mart-1 27-35 es SE . ID N0.:558 FLPSDFFPSV HBV cA 18-27 SE . ID N0.:559 Motif unknownAAGIGILTV Meland A/Mart-1 27-35 T cell a ito SE . ID N0.:560 es FLPSDFFPSV HBV cA 18-27 SEQ. ID N0.:561 AAGIGILTV Melan A/Mart-1 27-35 SE . ID N0.:562 ALLAVGATK Pmel17 100 17-25 SE . ID N0.:563 T cell a ito R L R D L L L I V HIV-1 41 768-778 es T R
SE . ID N0.:564 VPLRPMTYK HIV-1 nef 73-82 SEQ. ID N0.:565) SE . ID N0.:566) RLRPGGKKK HIV- 1 a 17 20-29 SE . ID N0.:567 ILRGSVAHK Influenza NP 265-273 SE . ID N0.:568 SEQ. ID N0.:569 SE .117 N0.:570 SE . ID N0.:571 SE . ID N0.:572 Motif unknownKIFSEVTLK Unknown; muta melanoma peptide ted I83L 1?5-183 T cell a SEQ. ID N0.:573 ito a YVNVNMGLK* HBV cA 88-96 (SE . ID N0.:574 T cell a IVTDFSVIK EBNA-4 416-424 ito es SEQ. 117 N0.:575) SEQ. ID N0.:576) (SE . ID N0.:577 AIF SSMTK HIV- I a 24 325-333 SE .117 N0.:578) QVPLRPMTYK HIV-1 nef 73-82 SE . ID N0.:579 SE . ID N0.:580) AAVDLSHFLKEK HIV-1 nef 83-94 (SE . ID N0.:581 K
SE . ID N0.:581 HLA-A24 S Y L D S G I H F* ~3-catenin, mutated (proto-onocogen) SE . 117 N0.:582 T cell a RYLKDQQLL HIV GP 41 583-591 ito es SE . ID N0.:583) AYGLDFYIL, P15 melanoma A 10- 18 SE . ID N0.:584) AFLPWHRLFL T osinase 206-215 SE . ID N0.:585) AFLPWHRLF Tyrosinase 206-214 SE . ID N0.:586 RYSIFFDY Ebna-3 246-253 SE . ID N0.:587 T cell a ETINEEAAEW HIV- 1 a 24 203-212 ito a SE . ID N0.:588 T cell a STLPETTVVRR HBV cA 141 -151 ito es SE . ID N0.:589 MSL R FLR ORF 3P- 75 294-321 b SE . ID N0.:590 LLPGGRPYR TRP t osinase rel. 197-205 SE . ID N0.:591 T cell a IVGLNKIVR HIV a 24 267-267-275 ito a SE . ID N0.:592 AAGIGILTV Melan A/Mart- 127 35 SE . ID N0.:593 Table 3 sets forth additional antigens useful in the invention that are available from the Ludwig Cancer Institute. The Table refers to patents in which the identified antigens can be found.
TRA refers to the tumor-related antigen and the LUD No. refers to the Ludwig Institute number.
Table 3 TRA LUD Patent Date Patent Peptide (Antigen) HLA
No. No. Issued MAGE-4 5293 5,405,94011 April EVDPASNTY HLA-AI
(SEQ. ID N0.:532) MAGE-41 5293 5,405,94011 April EVDPTSNTY HLA-A
(SEQ ID N0:533) MAGE-5 5293 5,405,94011 April EADPTSNTY HLA-A
(SEQ ID N0:534) MAGE-51 5293 5,405,9401 1 April EADPTSNTY HLA-A
(SEQ ID N0:534) MAGE-6 5294 5,405,940I 1 April EVDPIGHVY HLA-AI
(SEQ ID N0:535) 5299.25,487,97430 January MLLAVLYCLL HLA-A2 (SEQ ID N0:536) 5360 5,530,09625 June 1996MLLAVLYCL HLA-B44 (SEQ ID N0:537) Tyrosinase5360.15,519,11721 May 1996 SEIWRDIDFA HLA-B44 (SEQ ID N0:538) SEIWRDIDF
(SEQ ID N0:539) Tyrosinase5431 5,774,31628 April XEIWRDIDF HLA-B44 (SEQ ID N0:540) MAGE-2 5340 5,554,72410 SeptemberSTLVEVTLGEV HLA-A2 (SEQ ID N0:541) LVEVTLGEV
(SEQ ID N0:542) V IFSKASEYL
(SEQ ID N0:543) IIVLAIIAI
(SEQ ID N0:544) (Continued) KIWEELSMLEV
(SEQ ID N0:545) TRA LUD Patent Date Patent Peptide (Antigen) HLA
No. No. Issued LIETSYVKV
(SEQ ID N0:546) 5327 5,585,46117 December FLWGPRALV HLA-A2 (SEQ ID NO: 547) TLVEVTLGEV
(SEQ ID N0:548) ALV ETSYV KV
(SEQ ID N0:549) MAGE-3 5344 5,554,50610 SeptemberK(WEELSVL HLA-A2 (SEQ ID N0:550) MAGE-3 5393 5,405,94011 April EVDPIGHLY HLA-Al (SEQ ID N0:551) MAGE 5293 5,405,94011 April EXDXSY HLA-Al (SEQ. ID N0.:552) (but not EADPTGHSY) (SEQ. ID N0.:553) E (A/V) D X5 Y
(SEQ. ID N0.:554) E(A/V)DPX4Y
(SEQ. ID N0.:555) E (A/V) D P (1/A/T) (SEQ. ID N0.:556) E (A/V) D P (I/A/T) (G/S) X2 Y
(SEQ. ID N0.:557) E (A/V) D P (1/A/T) (G/S) (H/N) X Y
E (A/V) DP (I/A/T) (G/S) (H/N) (L/T/V) Y
(SEQ. I I) N0.:559) MACE-I 5361 5,558.99524 SeptemberELHSAYGEPRKLLTQD HLA-C
(SEQ ID N0:560) Clone EHSAYGEPRKLL
(SEQ ID N0:561 ) SAYGEPRKL
(SEQ ID N0:562) MAGE-1 5253.4TBA TBA EADPTGHSY HLA-A
I
(SEQ ID N0:563) TRA LUD Patent Date Patent Peptide (Antigen) HLA
No. No. Issued BAGS 5310.1TBA TBA MAARAVFLALSAQLLQARLMKEHLA-C
(SEQ ID N0:564) Clone MAARAVFLALSAQLLQ HLA-C
(SEQ ID N0:565) Clone AARAVFLAL HLA-C
(SEQ ID N0:566) Clone GAGE 5323.25,648,22615 July 1997YRPRPRRY HLA-CW6 (SEQ. ID N0.:567) Table 4 Source Protein AA MHC T cell epitope Ref.
PositionmoleculesMHC
li and Anti en syntheticsyntheticsyntheticHLA-A2 ALFAAAAAV Parker, et peptides peptidespeptides al., - "Scheme for ranking potential HLA-A2 binding peptides based onindependent binding of individual peptide side-chains,"
J.
Immunol.
152:163-175 " GIFGGVGGV "
" GLDKGGGV "
" GLFGGFGGV "
" GLFGGGAGV "
" GLFGGGEGV "
" GLFGGGFGV "
" GLFGGGGGL "
" GLFGGGGGV "
" GLFGGGVGV "
" GLFGGVGGV "
" GLFGGVGKV "
" GLFKGVGGV "
" GLGGGGFGV "
" GLLGGGVGV "
" GLYGGGGGV "
" GMFGGGGGV "
" GMFGGVGGV "
" GQFGGVGGV "
" GVFGGVGGV "
" KLFGGGGGV "
" KLFGGVGGV "
" AILGFVFTL "
" GAIGFVFTL "
" GALGFVFTL "
" GELGFVFTL "
" GIAGFVFTL "
" GIEGFVFTL "
" GILAFVFTL "
" GILGAVFTL "
" GILGEVFTL "
" GILFGAFTL "
" GILGFEFTL "
" GILGFKFTL "
" GILGFVATL "
" GILGFVETL "
" GILGFVFAL "
" GIL,GFVFEL "
" GILGFVFKL "
" GILGFVFTA "
" GILGFVFTL "
" GILGFVFVL "
" GILGFVKTL "
" GILGKVFTL "
" GILKFVFTL "
" GILPFVFTL "
" GIVGFVFTL "
" GKLGFVFTL "
" GLLGFVFTL "
" G LGFVFTL "
" KALGFVFTL "
" KILGFVFTL "
" KILGKVFTL "
" AILLGVFML "
" AlYKRWIIL "
" ALFFFDIDL "
" ATVELLSEL "
" CLFGYPVYV "
" FIFPNYTIV "
" IISLWDS L "
" ILASLFAAV "
" ILESLFAAV "
" KLGEFFN M "
" KLGEFYN M "
" LLFGYPVYV "
" LLWKGEGAV "
" LMFGYPVYV "
" LNFGYPVYV "
" LQFGYPVYV "
" NIVAHTFKV "
" NLPMVATV "
" QMLLAIARL "
" QMWQARLTV "
" RLLQTGIHV "
" RLVNGSLAL "
" SLYNTVATL "
" TLNAWVKVV "
" WLYRETCNL j " YLFKRMIDL "
" GAFGGVGGV "
" GAFGGVGGY "
" GEFGGVGGV "
" GGFGGVGGV "
" GIFGGGGGV "
" GIGGFGGGL "
" GIGGGGGGL "
" GLDGGGGGV "
" GLDGKGGGV "
" GLDKKGGGV "
" GLFGGGFGF "
" GLFGGGFGG "
" GLFGGGFGN "
" GLFGGGFGS "
" GLFGGGGGI "
" GLFGGGGGM "
" GLFGGGGGT "
" GLFGGGGGY "
" GLGFGGGGV "
" GLGGFGGGV "
" GLGGGFGGV "
" GLGGGGGFV "
" GLGGGGGGY "
" GLGGGVGGV "
" GLLGGGGGV "
" GLPGGGGGV "
" GNFGGVGGV "
" GSFGGVGGV "
" GTFGGVGGV "
" AGNSAYEYV "
" GLFPGQFAY "
" HILLGVFML "
" ILESLFRAV "
" KKKYKLKHI "
" MLASIDLKY "
" MLERELVRK "
" KLFGFVFTV "
" ILDKKVEKV "
" ILKEPVHGV "
" ALFAAAAAY "
" GIGFGGGGL "
" GKFGGVGGV "
" GLFGGGGGK "
" EILGFVFTL "
" GIKGFVFTL "
" GQLGFVFTK I "
" ILGFVFTLT "
" KII,GFVFTK "
" KKLGFVFTL "
" KLFEKVYNY "
" LRFGYPVYV "
Human HSP60 140-148 HLA-B27 IRRGVMLAV Rammensee et al. I 997 " " 369-377 " KRI EIIEQ "
" " 469-477 " KRTLKIPAM "
YersiniaHSP60 35-43 " GRNVVLDKS "
" " 117-125 " KRGIDKAVI "
" " 420-428 " IRAASAITA "
" HSP 60 284-292 HLA- RRKAMFEDI 169 B*2705 P.falci LSA-1 1850-1857HLA-B3501KPKDELDY 170 arum Influenza 379-387 HLA- LELRSRYWA 183 NP B *4402 Tum-P35B 4-13 HLA-Dd GPPHSNNFGY 230 RotavirusVP7 33-40 IIYRFLLI 262 OGDH 104-112 H2-Ld QLSPYPFDL 253 TRP-2 181-188 p287 VYDFFVWL 284 DEAD box 547-554 p287 SNFVFAGI 283 Vector p287 SVVEFSSL 260 "artefact"
Epiope p287 AHYLFRNL 278 mimic of tumor A
" THYLFRNL "
Epitope " LNIYNTL 279 mimic of H-3 miHA
"
" LIYEFNTL "
" IPYIYNTL "
" IIYII'IIRL "
" LIYIFNTL "
HBV cA 93-100 " MGLKFR L 280 Human autoantigen51-58 " 1MIKFRNRL 281 LA
Mouse UTY H2Db WMHIINMDLI 303 rotein Mouse 53 232-240 " KYMCNSSCM 302 MURINE MDM2 441-449 " GRPKNGCIV 277 Epitope " AQHPNAELL 278 mimic of natural MuLV 75-83 " CCLCLTVFL 301 gag75K
P. CSP 375-383 p290 YENDIEKK 315 Falci arum " " 371-379 " DELDYENDI 315 HIV -1RT 206-214 " TEMEKEGKI 316 Rabies NS 197-205 VEAEIAH I 309, 310 InfluenzaNS1 152-160 " EEGANGEI 304 A
Murine SMCY 291 TENSGKDI 317 MHC class3-11 p293 AMAPRTLLL 318 1 leader NDlal 1-12 293 FFINILTLLVP 323 ha ND Beta 1-12 293 FFINIZTLLVP 323 ND al 1-17 " FFINILTLLVPILIAM324 ha ND Beta 1-17 " FFINALTLLVPILIAM"
COI 1-6 " FINRW 325 mitochondri al L. LemA 1-6 " IGWII 326 monocytoge nes SN gag 179-190 Mamu-A*O1EGCTPYDINQML 334 5,554,506 " IMPKAGLLI "
" KIWEELSVL "
" ALVETSYVKV "
" ThrLeuValGluValThrL"
euGl GIuVaI
" AlaLeuSerArgLysValA"
laGIuLeu " IleMetProLysAlaGIyLe"
uLeuIle " LysIleTrpGluGluLeuSe"
rValLeu " AlaLeuVaIGIuThrSerT"
yrValLysVa1 peptides HLA-A2 Lys Gly Ile 5,989,565 Leu Gly which Phe Val Phe bind Thr Leu to MHCs Thr Val " Gly Ile Ile "
Gly Phe Val Phe Thr Ile " Gly Ile Ile "
Gly Phe Val Phe Thr Leu " Gly Ile Leu "
Gly Phe Val Phe Thr Leu " Gly Leu Leu "
Gly Phe Val Phe Thr Leu " XXTVXXGVX, "
X=Leu or Ile " Ile Leu Thr "
Val Ile Leu Gl Val Leu " Tyr Leu Glu "
Pro Gly Pro Val Thr Ala " Gln Val Pro "
Leu Arg Pro Met Thr T r L s " Asp Gly Leu "
Ala Pro Pro Gln His Leu Ile Arg " Leu Leu Gly "
Arg Asn Ser Phe Glu Val Peptides HLA-C GluHisSerAlaTyrGlyG5,558,995 from clone luProArgLysLeuLeuTh MAGE-1 rGlnAs Leu " GluHisSerAlaTyrGlyG"
luProAr LysLeuLeu " SerAlaTyrGlyGluProA"
rgLysLeu GAGE HLA-Cw6 TyrArgProArgProArgA5,648,226 rgTyr " ThrTyrArgProArgProA"
rgArgT r " TyrArgProArgProArgA"
rgTyrV al " ThrTyrArgProArgProA"
r Ar T Val " ArgProArgProArgArgT"
rValGlu " MetSerTrpArgGlyArgS"
erThrTyrArgProArgPro ~g~g " ThrTyrArgProArgProA"
rgArgTyrV alGluProPro GluMetIle MAGE HLA-A1, Isolated nonapeptide5,405,940 primarilyhaving Glu at its N
terminal, Tyr at its C-terminal, and Asp at the third residue from its N terminal, with the proviso that said isolated nonapeptide is not Glu Ala Asp Pro Thr Gly His Ser Tyr (SEQ ID NO:
1 ), and wherein said isolated nonapeptide binds to a human leukocyte antigen molecule on a cell to form a complex, said complex rovokin 1 sis of said cell by a cytolytic T
cell specific to said complex " GluValValProIleSerHis"
LeuT r " GluValValArgIleGlyHi"
sLeuT r " GluValAspProIleGlyHi"
sLeuT
" GluValAspProAlaSerA"
snThrTyr " GluValAspProThrSerA"
snThrT r " GluAlaAspProThrSerA"
snThrTyr " GluValAspProIleGlyHi"
sValTyr " GAAGTGGTCCCCAT "
CAGCCACTTGTAC
" GAAGTGGTCCGCA "
TCGGCCACTTGTAC
" GAAGTGGACCCCA "
TCGGCCACTTGTAC
" GAAGTGGACCCCG "
CCAGCAACACCTAC
" GAAGTGGACCCCA "
CCAGCAACACCTAC
" GAAGCGGACCCCA "
CCAGCAACACCTAC
" GAAGCGGACCCCA "
CCAGCAACACCTAC
" GAAGTGGACCCCA "
TCGGCCACGTGTAC
" GluAlaAspProThrGly"
HisSer " AlaAspProTrpGlyHisS"
erT
MAGE HLA-A2 SerThrLeuValGluValT5,554,724 a tides hrLeuGl GluVa1 " " LeuValGluValThrLeu"
Gl GIuVaI
" " LysMetValGluLeuVa1"
HisPheLeu " " ValIlePheSerLysAlaSe"
rGluT rLeu " " TyrLeuGlnLeuValPhe"
Gl IleGluVa1 " " GInLeuValPheGlyIleG1"
uValVal " " GInLeuValPheGlyIleG1"
uValValGluVal " " IleIleValLeuAlaIleIleA"
laIle " " LysIleTrpGluGluLeuSe"
rMetLeuGluVal " " AlaLeuIleGluThrSerTy"
rValLysVal " " LeuIleGluThrSerTyrVa"
ILysVal " " GlyLeuGluAlaArgGly"
GluAlaLeuG1 Leu " " GlyLeuGIuAlaArgGly"
GIuAlaLeu " " AlaLeuGlyLeuValGly"
AlaGlnAla " " GIyLeuValGlyAlaGln"
AIaProAla " " AspLeuGluSerGluPhe"
GlnAlaAla " " AspLeuGluSerGluPhe"
GlnAlaAlaIle " " AlaIleSerArgLysMetV"
alGluLeuVa1 " " AlaIleSerArgLysMetV"
aIGIuLeu " " LysMetValGluLeuVa1"
HisPheLeuLeu " " LysMetValGluLeuVal"
HisPheLeuLeuLeu " " LeuLeuLeuLysTyrArg"
AlaAr GluProVa1 " " LeuLeuLysTyrArgAla"
Ar GluProVa1 " " ValLeuArgAsnCysGln"
As PhePheProVal " " TyrLeuGInLeuValPhe"
Gl IleGluValVa1 " " GlyIleGluValValGluV"
aIVaIProIle " " ProIleSerHisLeuTyrIle"
LeuVal " " HisLeuTyrIleLeuValTh"
rC sLeu " " HisLeuTyrIleLeuValTh"
rC sLeuGl Leu " " TyrIleLeuValThrCysLe"
uGl Leu " " CysLeuGlyLeuSerTyr"
As Gl Leu " " CysLeuGlyLeuSerTyr"
As G1 LeuLeu " " ValMetProLysThrGIyL"
euLeuIle " " ValMetProLysThrGIyL"
euLeuIlelle " " ValMetProLysThrGlyL"
euLeuIleIleVal " " GlyLeuLeuIleIleValLe"
uAlaIle " " GlyLeuLeuIleIleValLe"
uAlaIleIle " " GlyLeuLeuIleIleValLe"
uAlaIleIleAla " " LeuLeuIleIleValLeuA1"
aIleIle " " LeuLeuIleIleValLeuA1"
aIleIleAla " " LeuLeuIleIleValLeuA1"
aIleIleAlaIle " " - LeuIleIleValLeuAlaIleI"
leAla " " LeuIleIleValLeuAlaIleI"
leAlaIle ' " " IIeIleAlaIleGluGlyAsp"
C sAla " " LysIleTrpGluGluLeuSe"
rMetLeu " " LeuMetGlnAspLeuVa1"
GlnGluAsnT rLeu " " PheLeuTrpGlyProArg"
AlaLeuIle " " LeuIleGluThrSerTyrVa"
1L sVal " " AlaLeuIleGluThrSerTy"
rValL sValLeu " " ThrLeuLysIleGlyGlyG1"
uProHisIle " " HisIleSerTyrProProLeu"
HisGluAr Ala " " GlnThrAlaSerSerSerSe"
rThrLeu " " GlnThrAlaSerSerSerSe"
rThrLeuVal " " ValThrLeuGlyGluValP"
roAlaAla " " ValThrLysAlaGluMetL"
euGluSerVa1 " " ValThrLysAlaGluMetL"
euGluSerValLeu " " VaIThrCysLeuGlyLeu"
SerTyrAs G1 Leu " " LysThrGlyLeuLeuIleI1"
eValLeu " " LysThrGIyLeuLeuIleIl"
eValLeuAla " " LysThrGlyLeuLeuIleI1"
eValLeuAlaIle " " HisThrLeuLysIleGlyGl"
GluProHisIle " " MetLeuAspLeuGlnPro"
GluThrThr Mage-3 HLA-A2 GlyLeuGluAlaArgGly5,585,461 a tides GluAlaLeu " " AlaLeuSerArgLysValA"
IaGluLeu " " PheLeuTrpGlyProArg"
AlaLeuVal " " ThrLeuValGluValThrL"
euGl GluVa1 " " AlaLeuSerArgLysValA"
laGluLeuVal " " AlaLeuValGluThrSerT"
rValL sVal Tyrosinase HLA-A2 TyrMetAsnGlyThrMet5,487,974 SerGlnVal " " MetLeuLeuAlaValLeu"
T sLeuLeu Tyrosinase HLA-A2 MetLeuLeuAlaValLeu5,530,096 T rC sLeu " " LeuLeuAlaValLeuTyr"
C sLeuLeu Tyrosinase HLA-A2 SerGluIleTrpArgAspIle5,519,117 and HLA-B44 As PheAlaHisGluAla " " SerGluIleTrpArgAspIle"
As Phe " " GluGluAsnLeuLeuAsp"
PheValAr Phe Melan EAAGIGIL,TV Jager, E.
et al.
A/MART-1 Granulocyte-macrophage-colony-stimulating Factor Enhances Immune Responses To Melanoma-'associated Peptides in vivo hit. J Cancer 67, 54-62 1996) T rosinase MLLAVLYCL "
" YMDGTMS V "
gp100/Pmel YLEPGPVTA "
" LLDGTATLRL "
Influenza GILGFVFTL "
matrix MAGE-1 EADPTGHSY "
FROM
DAVID'S
LIST
BAGE HLA-C MAARAVFLALSAQL "
LQARLMKE
" " MAARAVFLALSAQL "
LQ
" " AARAVFLAL "
InfluenzaPR8 NP 147-154 Kd IYQRIRALV Falk et al., Allele-specific motifs revealed by sequencing of self peptides eluted from MHC molecules SELF P815 " SYFPEITHI "
PEPTIDE
InfluenzaJap HA " IYATVAGSL "
VYQILAIYA "
" " ~~ IYSTVASSL "
" JAP HA ~~ LYQNVGTYV "
HLA-A24 ~~ RYLENQKRT "
HLA-Cw3 " RYLKNGKET "
P815 " KYQAVTTTL "
PlasmodiumCSP " SYIPSAEKI "
berghen PlasmodiumCSP " SYVPSAFQI "
yoelli VesicularNP 52-59 Kb RGYVYQGL "
stomatitis viruse Ovalbumin " SIINFEKL "
Sandal NP 321-332 " APGNYPAL "
Virus VPYGSFKHV Morel et al., Processing of some antigens by the standard proteasome but not by the immunoproteaso me results in poor presentation by dendritic cells, Immunity, vol.
12:107-117, 2000.
MOTIFS
influenzaPR8 NP Kd restrictedTYQRTRALV 5,747,269 peptide motif self P815 " SYFPEITHI "
a tide influenzaJAP HA " IYATVAGSL "
influenzaJAP HA " VYQILAIYA "
influenzaPR8 HA " IYSTVASSL "
influenzaJAP HA " LYQNVGTYV "
HLA-A24 RYLENGKETL "
HLA-Cw3 RYLKNGKETL "
P815 " KYQAVTTTL "
tumour antigen PlasmodiumCSP " SYIPSAEKI "
ber hei PlasmodiumCSP ~ " SYVPSAEQI "
oeli influenzaNP Db - ASNENMETM "
restricted peptide motif adenovirusElA " SGPSNTPPEI "
lymphocytic " SGVENPGGYCL "
choriomenin gitis simian 40 T " SAINNY . . . "
virus HIV reverse HLA-A2.1-ILKEPVHGV "
transcriptase restricted peptide motif influenza " GILGFVFTL "
matrix rotein influenzainfluenza " ILGFVFTLTV "
matrix rotein HIV Ga rotein FL SRPEPT "
HIV Ga rotein AM MLKE . . "
HIV Ga rotein PIAPG MRE "
HIV Ga rotein MKDCTER "
HLA- VYGVIQK "
A*0205-restricted peptide motif Table S
VSV-NP a tide 49-62 LCMV-NP a tide 118-132 LCMV 1 co rotein a tide. 33-41 ISN LTLDSNTKYFHKLN
ISNQLTLDSNTKYFHKL
ISNQLTLDSNTKYFHK
VDTFLEDVKNLYHSEA
KPRAIVVDPVHGFMY
K TISPDYRNMI
Y DFIMDPKEKDKV
LLSFVRDLN YRADI
LPKPPKPV SKMRMATPL
LPKPPKPV SKMRMATPLLMQALP
LPKPPKPVSKMRMATPLLM ALPM
PKPPKP V SKMRMATPL
PKPPKPVSKMRMATPLLM A
KPPKPVSKMRMATPLLMQ
KPPKPVSKMRMATPLLMQALPM
VDDTQFVRFDSDAAS
ATKYGNMTEDHVMHLLQNA
VFLLLLADKVPETSLS
LNKILLDE A WK
GPPKLDIRKEEK IMIDIFH
GPPKLDIRKEEK IM>DIFHP
GFKAIRPDKKSNPIIRTV
YANILLDRRVP TDMTF
NLFLKSDGRIKYTLNKNSLK
IPDNLFLKSDGRIKYTLNKN
IPDNLFLKSDGRIKYTLNK
IPDNLFLKSDGRIKYTLN
NLFLKSDGRIKYTLNK
NLFLKSDGRIKYTLN
VTTLNSDLKYNALDLTN
VGSDWRFLRGYHQYA
[0078] Still further embodiments are directed to methods, uses, therapies and compositions related to epitopes with specificity for MHC, including, for example, those listed in Tables 6-10. Other embodiments include one or more of the MHCs listed in Tables 6-10, including combinations of the same, while other embodiments specifically exclude any one or more of the MHCs or combinations thereof. Tables 8-10 include frequencies for the listed HLA antigens.
Table 6 Class I MHC Molecules Class I
Human HLA-A*0101 HLA-A*0201 HLA-A*0202 HLA-A*0203 HLA-A*0204 HLA-A*0205 HLA-A*0206 HLA-A*0207 HLA-A*0209 HLA-A*0214 HLA-A*0301 HLA-A* 11 O 1 HLA-A*2902 HLA-A*3101 HLA-A*3302 HLA-A*6801 HLA-A*6901 HLA-B*0702 HLA-B*0703 HLA-B *0704 HLA-B*0705 HLA-B*1501 (B62) HLA-B *2702 HLA-B*2704 HLA-B*2705 HLA-B*2709 HLA-B*3501 HLA-B*3502 HLA-B*3701 HLA-B*3801 HLA-B*39011 HLA-B *3902 HLA-B*40012 (B60) HLA-B*4006 (B61) HLA-B*4402 HLA-B*4403 HLA-B*4501 HLA-B *4601 HLA-B*5101 HLA-B * 5102 HLA-B*5103 HLA-B*5201 HLA-B*5301 HLA-B*5401 HLA-B*5501 HLA-B*5502 HLA-B*5601 HLA-B*5801 HLA-B*6701 HLA-B*7301 HLA-B*7801 HLA-Cw*0102 HLA-Cw*0301 HLA-Cw*0304 HLA-Cw*0401 HLA-Cw *0601 HLA-Cw*0602 HLA-Cw*0702 HLA-Cw8 HLA-Cw*1601 M
HLA-G
Murine H2-Kd H2-Dd H2-Ld H2-Kb H2-Db H2-K'' H2-K'""' Qa-la Qa-2 Rat RT 1.Aa RT 1.A' Bovine Bota-Al l Bota-A20 Chicken Chimpanzee Patr-A*04 Patr-A* 11 Patr-B*01 Patr-B * 13 Patr-B * 16 Baboon Papa-A*06 Macaque Mamu-A*01 Swine SLA (haplotype d/d) Virus homolog hCMV class I homolog UL18 Table 7 Class I MHC Molecules Class I
Human HLA-Al HLA-A*0101 HLA-A*0201 HLA-A*0202 HLA-A*0204 HLA-A*0205 HLA-A*0206 HLA-A*0207 HLA-A*0214 HLA-A* 11 O 1 HLA-A*2902 HLA-A*3101 HLA-A*3302 HLA-A*6801 HLA-A*6901 HLA-B*0702 HLA-B *0703 HLA-B*0704 HLA-B *0705 HLA-B*1501 (B62) HLA-B *2702 HLA-B *2705 HLA-B*3501 HLA-B*3502 HLA-B*3701 HLA-B*3801 HLA-B*39011 HLA-B*3902 HLA-B*40012 (B60) HLA-B*4006 (B61) HLA-B*4402 HLA-B*4403 HLA-B *4641 HLA-B*5101 HLA-B*5102 HLA-B*5103 HLA-B*5201 HLA-B*5301 HLA-B * 5401 HLA-B*5501 HLA-B*5502 HLA-B*5601 HLA-B*5801 HLA-B *6701 HLA-B*7301 HLA-B*7801 HLA-Cw*0102 HLA-Cw*0301 HLA-Cw*0304 HLA-Cw*0401 HLA-Cw*0601 HLA-Cw*0602 HLA-Cw*0702 HLA-G
Murine H2-K'' H2-Dd H2-Ld H2-Kb H2-Db H2-Kk H2-K'""' Qa-2 Rat RTl .A~
RT1.A~
Bovine Bota-Al l Bota-A20 Chicken Virus homolog hCMV class I homolog UL18 Table 8 [0079) Estimated gene frequencies of HLA-A antigens CAU AFR ASI LAT NAT
Antigen G~ SEb Gf SE Gf SE Gf SE Gf SE
A1 15.18430.04895.72560.07714.48180.08467.40070.097812.03160.2533 A2 28.65350.061918.88490.131724.63520.179428.11980.170029.34080.3585 A3 13.38900.04638.44060.09252.64540.06558.07890.101911.02930.2437 A28 4.46520.02809.92690.09971.76570.05378.94460.10675.38560.1750 A36 0.02210.00201.88360.04480.01480.00490.15840.01480.15450.0303 A23 1.82870.018110.20860.10100.32560.02312.92690.06281.99030.1080 A24 9.32510.03952.96680.056022.03910.172213.26100.127112.66130.2590 A9 unsplit0.08090.00380.03670.00630.08580.01190.05370.00860.03560.0145 A9 total11.23470.042913.21210.112822.45050.173316.24160.138214.68720.2756 A25 2.11570.01950.43290.02160.09900.01281.19370.04041.45200.0924 A26 3.87950.02622.82840.05474.66280.08623.26120.06622.42920.1191 A34 0.15080.00523.52280.06101.35290.04700.49280.02600.31500.0432 A43 0.00180.00060.03340.00600.02310.00620.00550.00280.00590.0059 A66 0.01730.00180.22330.01550.04780.00890.03990.00740.05340.0178 A10 unsplit0.07900.00380.09390.01010.12550.01440.06470.00940.02980.0133 A10 total6.24410.03287.13480.08506.31110.09935.05780.08164.28530.1565 A29 3.57960.02523.20710.05821.12330.04294.51560.07743.43450.1410 A30 2.50670.021213.09690.11292.20250.05984.48730.07722.53140.1215 A31 2.73860.02211.65560.04203.60050.07614.83280.08006.08810.1855 A32 3.69560.02561.53840.04051.03310.04112.70640.06042.55210.1220 A33 1.20800.01486.56070.08229.27010.11912.65930.05991.07540.0796 A74 0.02770.00221.99490.04610.05610.00960.20270.01670.10680.0252 A19 unsplit0.05670.00320.20570.01490.09900.01280.12110.01290.04750.0168 A19 total13.81290.046828.25930.150417.38460.155519.52520.148115.83580.2832 AX 0.82040.02974.95060.09632.99160.11771.63320.08781.84540.1925 Gene frequency.
bStandard error.
Table 9 Estimated gene frequencies for HLA-B antigens CAU AFR ASI LAT NAT
AntigenG~ SE Gf SE Gf SE Gf SE Gf SE
B7 12.17820.044510.59600.10244.26910.08276.44770.091810.98450.2432 B8 9.40770.03973.83150.06341.33220.04673.82250.07158.57890.2176 B 13 2.30610.02030.81030.02954.92220.08861.26990.04161.74950.1013 B 14 4.34810.02773.03310.05660.50040.02875.41660.08462.98230.1316 B 18 4.79800.02903.20570.05821.12460.04294.23490.07523.34220.1391 B27 4.38310.02781.29180.03722.23550.06032.37240.05675.19700.1721 B35 9.66140.04028.51720.09278.12030.112214.65160.132910.11980.2345 B37 1.40320.01590.59160.02521.23270.04490.78070.03270.97550.0759 B41 0.92110.01290.81830.02960.13030.01471.28180.04180.47660.0531 B42 0.06080.00335.69910.07680.08410.01180.58660.02840.28560.0411 B46 0.00990.00130.01510.00404.92920.08860.02340.00570.02380.0119 B47 0.20690.00610.13050.01190.09560.01260.18320.01590.21390.0356 B48 0.08650.00400.13160.01192.02760.05751.59150.04661.02670.0778 B53 0.46200.009210.95290.10390.43150.02661.69820.04811.08040.0798 CAU AFR ASI LAT NAT
AntigenGf SE Gf SE Gf SE Gf SE Gf SE
B59 0.00200.00060.00320.00190.42770.02650.00550.00280' B67 0.00400.00090.00860.00300.22760.01940.00550.00280.00590.0059 B70 0.32700.00777.35710.08660.89010.03821.92660.05120.69010.0639 B73 0.01080.00140.00320.00190.01320.00470.02610.00600' B51 5.42150.03072.59800.05257.47510.10806.81470.09436.90770.1968 B52 0.96580.01321.37120.03833.51210.07522.24470.05520.69600.0641 B5 unsplit0.15650.00530.15220.01280.12880.01460.15460.01460.13070.0278 B5 total6.54380.04354.12140.074711.11600.15049.21410.13247.73440.2784 B44 13.48380.04657.01370.08475.68070.09489.92530.112111.80240.2511 B45 0.57710.01024.80690.07080.18160.01731.88120.05060.76030.0670 B12 0.07880.00380.02800.00550.00490.00290.01930.00510.06540.0197 unsplit B12 14.14400.047411.84860.10725.86730.096311.82580.121012.62810.2584 total 6.9421 B62 5.91170.03201.52670.04049.22490.11904.18250.0747 p,1973 0.3738 B63 0.43020.00881.88650.04480.44380.02700.80830.0333 p,p471 0.0356 B75 0.01040.00140.02260.00491.96730.05660.11010.0123 0.0145 p B76 0.00260.00070.00650.00260.08740.01200.00550.0028 B77 0.00570.00100.01190.00360.05770.00980.00830.0034 0.0059 0.0059 B 15 0.13050.00490.06910.00860.43010.02660.18200.0158 p,p206 unsplit 0.0715 B15 6.49100.03343.52320.060812.21120.13445.29670.0835 p,2035 total 7.4290 B38 2.44130.02090.33230.01893.28180.07281.96520.05171.10170.0806 B39 1.96140.01881.28930.03712.03520.05766.30400.09094.55270.1615 B16 0.06380.00340.02370.00510.06440.01030.12260.01300.05930.0188 unsplit B16 4.46670.02801.64530.04195.38140.09218.39170.10365.71370.1797 total B57 3.59550.02525.67460.07662.57820.06472.18000.05442.72650.1260 B58 0.71520.01145.95460.07844.01890.08031.24810.04130.93980.0745 B 17 0.28450.00720.32480.01870.37510.02480.14460.01410.26740.0398 unsplit B17 4.59520.028411.95400.10766.97220.10413.57270.06913.93380.1503 total B49 1.64520.01722.62860.05280.24400.02002.33530.05621.54620.0953 B50 1.05800.01380.86360.03040.44210.02701.88830.05070.78620.0681 B21 0.07020.00360.02700.00540.01320.00470.07710.01030.03560.0145 unsplit B21 2.77330.02223.51920.06080.69930.03394.30070.07552.36800.1174 total B54 0.01240.00150.01830.00442.68730.06600.02890.00630.05340.0178 B55 1.90460.01850.48950.02292.24440.06040.95150.03611.40540.0909 B56 0.55270.01000.26860.01700.82600.03680.35960.02220.33870.0448 B22 0.16820.00550.04960.00730.27300.02120.03720.00710.12460.0272 unsplit B22 2.08520.02170.82610.02976.03070.09711.37710.04331.92210.1060 total B60 5.22220.03021.52990.04048.32540.11352.25380.05535.72180.1801 B61 1.19160.01470.47090.02256.20720.09894.66910.07882.60230.1231 B40 0.26960.00700.03880.00650.32050.02300.24730.01840.22710.0367 unsplit B40 6.68340.03382.03960.046514.85310.14627.17020.09638.55120.2168 total BX 1.09220.02523.52580.08023.87490.09882.52660.0807( 1.98670.1634 ~
Gene frequency. bStandard error. °The observed gene count was zero.
Table 10.
Estimated gene frequencies of HLA-DR antigens CAU AFR ASI LAT NAT
Antigen G~ SEb Gf Gf SE Gf SE Gf SE
SE
DR1 10.22790.04136.82000.08323.46280.07477.98590.10138.25120.2139 DR2 15.24080.049116.23730.122218.61620.160811.23890.118215.39320.2818 DR3 10.87080.042413.30800.11244.72230.08677.89980.100810.25490.2361 DR4 16.75890.05115.70840.076515.46230.149020.53730.152019.82640.3123 DR6 14.39370.047918.61170.129113.44710.140417.02650.141114.80210.2772 DR7 13.28070.046310.13170.09976.92700.104010.67260.11 10.42190.2378 DR8 2.88200.02276.26730.08006.54130.10139.77310.11106.00590.1844 DR9 1.06160.01392.96460.05599.75270.12181.07120.03832.86620.1291 DR10 1.47900.01632.03970.04652.23040.06021.80440.04951.08960.0801 DR11 9.31800.039610.61510.10184.73750.08697.04110.09555.31520.1740 DR12 1.90700.01854.11520.065510.13650.12391.72440.04842.01320.1086 DR5 unsplit1.21990.01492.29570.04931.41180.04801.82250.04981.67690.0992 DR5 total12.44490.004517.02600.124316.28580.151610.58800.11489.00520.2218 DRX 1.35980.03420.88530.07602.55210.10891.40230.09302.08340.2037 ''Gene frequency.
bStandard error.
[0080] It can be desirable to express housekeeping peptides in the context of a larger protein. Processing can be detected even when a small number of amino acids are present beyond the terminus of an epitope. Small peptide hormones are usually proteolytically processed from longer translation products, often in the size range of approximately 60-120 amino acids. This fact has led some to assume that this is the minimum size that can be efficiently translated. In some embodiments, the housekeeping peptide can be embedded in a translation product of at least about 60 amino acids, in others 70, 80, 90 amino acids, and in still others 100, 110 or 120 amino acids, for example. In other embodiments the housekeeping peptide can be embedded in a translation product of at least about 50, 30, or 15 amino acids.
[0081] Due to differential proteasomal processing, the immunoproteasome of the pAPC
produces peptides that are different from those produced by the housekeeping proteasome in peripheral body cells. Thus, in expressing a housekeeping peptide in the context of a larger protein, it is preferably expressed in the pAPC in a context other than its full-length native sequence, because, as a housekeeping epitope, it is generally only efficiently processed from the native protein by the housekeeping proteasome, which is not active in the pAPC. In order to encode the housekeeping epitope in a DNA sequence encoding a larger polypeptide, it is useful to find flanking areas on either side of the sequence encoding the epitope that permit appropriate cleavage by the immunoproteasome in order to liberate that housekeeping epitope. Such a sequence promoting appropriate processing is referred to hereinafter as having substrate or liberation sequence function.
Altering flanking amino acid residues at the N-terminus and C-terminus of the desired housekeeping epitope can facilitate appropriate cleavage and generation of the housekeeping epitope in the pAPC.
Sequences embedding housekeeping epitopes can be designed de novo and screened to determine which can be successfully processed by immunoproteasomes to liberate housekeeping epitopes.
[0082] Alternatively, another strategy is very effective for identifying sequences allowing production of housekeeping epitopes in APC. A contiguous sequence of amino acids can be generated from head to tail arrangement of one or more housekeeping epitopes.
A construct expressing this sequence is used to immunize an animal, and the resulting T
cell response is evaluated to determine its specificity to one or more of the epitopes in the array. These immune responses indicate housekeeping epitopes that are processed in the pAPC
effectively. The necessary flanking areas around this epitope are thereby defined. The use of flanking regions of about 4-6 amino acids on either side of the desired peptide can provide the necessary information to facilitate proteasome processing of the housekeeping epitope by the immunoproteasome.
Therefore, a substrate or liberation sequence of approximately 16-22 amino acids can be inserted into, or fused to, any protein sequence effectively to result in that housekeeping epitope being produced in an APC. In some embodiments, a broader context of a substrate sequence can also influence processing. In such embodiments, comparisons of a liberaton sequence in a variety of contexts can be useful in further optimizing a particular substrate sequence. In alternate embodiments the whole head-to-tail array of epitopes, or just the epitopes immediately adjacent to the correctly processed housekeeping epitope can be similarly transferred from a test construct to a vaccine vector.
[0083] In a preferred embodiment, the housekeeping epitopes can be embedded between known immune epitopes, or segments of such, thereby providing an appropriate context for processing. The abutment of housekeeping and immune epitopes can generate the necessary context to enable the immunoproteasome to liberate the housekeeping epitope, or a larger fragment, preferably including a correct C-terminus. It can be useful to screen constructs to verify that the desired epitope is produced. The abutment of housekeeping epitopes can generate a site cleavable by the immunoproteasome. Some embodiments of the invention employ known epitopes to flank housekeeping epitopes in test substrates; in others, screening as described below is used, whether the flanking regions are arbitrary sequences or mutants of the natural flanking sequence, and whether or not knowledge of proteasomal cleavage preferences are used in designing the substrates.
[0084] Cleavage at the mature N-terminus of the epitope, while advantageous, is not required, since a variety of N-terminal trimming activities exist in the cell that can generate the mature N-terminus of the epitope subsequent to proteasomal processing. It is preferred that such N-terminal extension be less than about 25 amino acids in length and it is further preferred that the extension have few or no proline residues. Preferably, in screening, consideration is given not only to cleavage at the ends of the epitope (or at least at its C-terminus), but consideration also can be given to ensure limited cleavage within the epitope.
[0085] Shotgun approaches can be used in designing test substrates and can increase the efficiency of screening. In one embodiment multiple epitopes can be assembled one after the other, with individual epitopes possibly appearing more than once. The substrate can be screened to determine which epitopes can be produced. In the case where a particular epitope is of concern, a substrate can be designed in which it appears in multiple different contexts.
When a single epitope appearing in more than one context is liberated from the substrate additional secondary test substrates, in which individual instances of the epitope are removed, disabled, or are unique, can be used to determine which are being liberated and truly confer substrate or liberation sequence function.
[0086] Several readily practicable screens exist. A preferred in vitro screen utilizes proteasomal digestion analysis, using purified immunoproteasomes, to determine if the desired housekeeping epitope can be liberated from a synthetic peptide embodying the sequence in question.
The position of the cleavages obtained can be determined by techniques such as mass spectrometry, HPLC, and N-terminal pool sequencing; as described in greater detail in U.S.
Patent Application Nos. 09/561,074, 09/560,465 and 10/117,937, and Provisional U.S. Patent Application Nos.
60/282,211, 60/337,017, and 60/363, 210.
[0087] Alternatively, in vivo and cell-based screens such as immunization or target sensitization can be employed. For immunization a nucleic acid construct capable of expressing the sequence in question is used. Harvested CTL can be tested for their ability to recognize target cells presenting the housekeeping epitope in question. Such targets cells are most readily obtained by pulsing cells expressing the appropriate MHC molecule with synthetic peptide embodying the mature housekeeping epitope. Alternatively, immunization can be carried out using cells known to express housekeeping proteasome and the antigen from which the housekeeping epitope is derived, either endogenously or through genetic engineering. To use target sensitization as a screen, CTL, or preferably a CTL clone, that recognizes the housekeeping epitope can be used.
In this case it is the target cell that expresses the embedded housekeeping epitope (instead of the pAPC during immunization) and it must express immunoproteasome. Generally, the cell or target cell can be transformed with an appropriate nucleic acid construct to confer expression of the embedded housekeeping epitope. Loading with a synthetic peptide embodying the embedded epitope using peptide loaded liposomes, or complexed with cationic lipid protein transfer reagents such as BIOPORTERTM (Gene Therapy Systems, San Diego, CA), represents an alternative.
[0088] Once sequences with substrate or liberation sequence function are identified they can be encoded in nucleic acid vectors, chemically synthesized, or produced recombinantly. In any of these forms they can be incorporated into immunogenic compositions. Such compositions can be used in vitro in vaccine development or in the generation or expansion of CTL
to be used in adoptive immunotherapy. In vivo they can be used to induce, amplify or sustain and active immune response.
The uptake of polypeptides for processing and presentation can be greatly enhanced by packaging with cationic lipid, the addition of a tract of cationic amino acids such as poly-L-lysine (Ryser, H.J.
et al., J. Cell Physiol. 113:167-178, 1982; Shen, W.C. & Ryser, H.J., Proc.
Natl. Aced. Sci. USA
75:1872-1876, 1978), the incorporation into branched structures with importation signals (Sheldon, K. et al., Proc. Natl. Aced. Sci. USA 92:2056-2060, 1995), or mixture with or fusion to polypeptides with protein transfer function including peptide earners such as pep-1 (Morris, M.C., et al., Nat.
Biotech. 19:1173-1176, 2001), the PreS2 translocation motif of hepatitis B
virus surface antigen, VP22 of herpes viruses, and HIV-TAT protein (Oess, S. & Hildt, E., Gene Ther.
7:750-758, 2000;
Ford, K.G., et al., Gene Ther. 8:1-4, 2001; Hung, C.F. et al., J. virol.
76:2676-2682, 2002; Oliveira, S.C., et a;. Hum. Gene Ther. 12:1353-1359, 2001; Normand, N. et al., J. Biol.
Chem. 276:15042-15050, 2001; Schwartz, J.J. & Zhang, S., Curr. Opin. Mol. Ther. 2:162-167, 2000; Elliot G., 7 Hare, P. Cell 88:223-233, 1997), among other methodologies. Particularly for fusion proteins the immunogen can be produced in culture and the purified protein administered or, in the alternative, the nucleic acid vector can be administered so that the immunogen is produced and secreted by cells transformed in vivo. In either scenario the transport function of the fusion protein facilitates uptake by pAPC.
EXAMPLES
Example 1 [0089] A recombinant DNA plasmid vaccine, pMA2M, which encodes one polypeptide with an HLA A2-specific CTL epitope ELAGIGIL,TV (SEQ ID NO. 1) from melan-A
(26-35A27L), and a portion (amino acids 31-96) of melan-A (SEQ ID NO. 2) including the epitope clusters at amino acids 31-48 and 56-69, was constructed. These clusters were previously disclosed in U.S.
Patent Application No. 09/561,571 entitled EPITOPE CLUSTERS. Flanking the defined melan-A
CTL epitope are short amino acid sequences derived from human tyrosinase (SEQ
ID NO. 3) to facilitate liberation of the melan-A housekeeping epitope by processing by the immunoproteasome.
In addition, these amino acid sequences represent potential CTL epitopes themselves. The cDNA
sequence for the polypeptide in the plasmid is under the control of promoter/enhancer sequence from cytomegalovirus (CMVp) (see Figure 1), which allows efficient transcription of messenger for the polypeptide upon uptake by APCs. The bovine growth hormone polyadenylation signal (BGH
polyA) at the 3' end of the encoding sequence provides a signal for polyadenylation of the messenger to increase its stability as well as for translocation out of nucleus into the cytoplasm for translation.
To facilitate plasmid transport into the nucleus after uptake, a nuclear import sequence (I~IIS) from simian virus 40 (SV40) has been inserted in the plasmid backbone. The plasmid carries two copies of a CpG immunostimulatory motif, one in the NIS sequence and one in the plasmid backbone.
Lastly, two prokaryotic genetic elements in the plasmid are responsible for amplification in E.coli, the kanamycin resistance gene (Kan R) and the pMB 1 bacterial origin of replication.
SUBSTRATE or LIBERATION sequence [0090] The amino acid sequence of the encoded polypeptide (94 amino acid residues in length) (SEQ ID NO. 4) containing a 28 amino acid substrate or liberation sequence at its N-terminus (SEQ ID NO. 5) is given below:
[0091] MLLAVLYCL-ELAGIGILTV-YMDGTMSQV-GILTVILGVLLLIGCWYCRRRNGYRALMDKSLHVGTQCALTRRCPQEGFDHRDSKVSLQEK
NCEPV
[0092] The first 9 amino acid residues are derived from tyrosinase~_9 (SEQ ID
NO. 6), the next ten constitute melan-A (26-35A27L) (SEQ )D NO. 1), and amino acid residues 20 to 29 are derived from tyrosinase369-377 (SEQ >D NO. 7). These two tyrosinase nonamer sequences both represent potential HLA A2-specific CTL epitopes. Amino acid residues 10-19 constitute melan-A
(26-35A27L) an analog of an HLA A2-specific CTL epitope from melan-A, EAAGIGILTV (SEQ ID
NO. 8), with an elevated potency in inducing CTL responses during in vitro immunization of human PBMC and in vivo immunization in mice. The segment of melan-A constituting the rest of the polypeptide (amino acid residues 30 to 94) contain a number of predicted HLA
A2-specific epitopes, including the epitope clusters cited above, and thus can be useful in generating a response to immune epitopes as described at length in the patent applications 'Epitope Synchronization in Antigen Presenting Cells' and 'Epitope Clusters'. This region was also included to overcome any difficulties that can be associated with the expression of shorter sequences. A drawing of pMA2M is shown in Figure 1.
Plasmid construction [0093] A pair of long complementary oligonucleotides was synthesized which encoded the first 30 amino acid residues. In addition, upon annealing, these oligonucleotides generated the cohensive ends of Afl II at the 5' end and that of EcoR I at the 3' end. The melan A3,_96 region was amplified with PCR using oligonucleotides carrying restriction sites for EcoR
I at the 5' end and Not I at the 3' end. The PCR product was digested with EcoR I and Not I and ligated into the vector backbone, described in Example 1, that had been digested with Afl II and Not I, along with the annealed oligonucleotides encoding the amino terminal region in a three-fragment ligation. The entire coding sequence was verified by DNA sequencing. The sequence of the entire insert, from the Afl II site at the 5' end to the Not I site at the 3' end is disclosed as SEQ
ID NO. 9. Nucleotides 12-293 encode the polypeptide.
Example 2 [0094] Three vectors containing melan-A (26-35A27L) (SEQ B7 NO. 1) as an embedded housekeeping epitope were tested for their ability to induce a CTL
response to this epitope in HLA-A2 transgenic HHD mice (Pascolo et al. J. Exp. Med. 185:2043-2051, 1997). One of the vectors was pMA2M described above (called pVAXM3 in Figure 3). In pVAXM2 the same basic group of 3 epitopes was repeated several times with the flanking epitopes truncated by differing degrees in the various repeats of the array. Specifically the cassette consisted o~
[0095] M-Tyr(5-9)-ELA-Tyr(369-373)-Tyr(4-9)-ELA-Tyr(369-374)-Tyr(3-9)-ELA-Tyr(369-375)-Tyr(2-9)-ELA
(SEQ ID NO. 10) [0096] where ELA represents melan-A (26-35A27L) (SEQ >D NO. 1). This cassette was inserted in the same plasmid backbone as used for pVAXM3. The third, pVAXMI is identical to pVAXM2 except that the epitope array is followed by an IRES (internal ribosome entry site for encephalomyocarditis virus) linked to a reading frame encoding melan-A 31-70.
[0097] Four groups of three HHD A2.1 mice were injected intranodally in surgically exposed inguinal lymph nodes with 25 pl of 1 mg/ml plasmid DNA in PBS on days 0, 3, and 6, each group receiving one of the three vectors or PBS alone. On day 14 the spleens were harvested and restimulated in vitro one time with 3-day LPS blasts pulsed with peptide (melan-A (26-35A27L)(SEQ ID NO. 1)). The in vitro cultures were supplemented with Rat T-Stim (Collaborative Biomedical Products) on the 3'd day and assayed for cytolytic activity on the 7'" day using a standard 51 Cr-release assay. Figures 2 to 5 show % specific lysis obtained using the cells immunized with PBS, pVAXMl, pVAXM2, and pVAXM3, respectively on T2 target cells and T2 target cells pulsed with melan-A (26-35A27L) (ELA) (SEQ ID NO. 1). All three vectors generated strong CTL
responses. These data indicated that the plasmids have been taken up by APCs, the encoded polypeptide has been synthesized and proteolytically processed to produce the decamer epitope in question (that is, it had substrate or liberation sequence function), and that the epitope became HLA-A2 bound for presentation. Also, an isolated variant of pVAXM2, that terminates after the 55'"
amino acid, worked similarly well as the full length version (data not shown).
Whether other potential epitopes within the expression cassette can also be produced and be active in inducing CTL
responses can be determined by testing for CTL activity against target cells pulsed with corresponding synthetic peptides.
Example 3 An NY-ESO-1 (SEQ ID NO. 11 ) SUBSTRATE/LIBERATION Sequence [0098] Six other epitope arrays were tested leading to the identification of a substrate/liberation sequence for the housekeeping epitope NY-ESO-1,57_165 (SEQ 117 NO. 12). The component epitopes of the arrays were:
[0099]SSX-24~-49: KASEKIFYV (SEQ ID NO. Array element 13) A
[O100JNY-ESO-1157-165SLLMWITQC (SEQ ID NO. Array element 12) B
[0101]NY-ESO-1 ~ TQCFLPVFL (SEQ m NO. Array element 63_ ~ ~ ~ 14) C
:
[0102]PSMA2gg_297: GLPS1PVHPI(SEQ ID NO. Array element 15) D
[0103]TYR4_9: AVLYCL (SEQ ID NO. Array element 16) E
[0104]The six arraysthe following had arrangements of elements after starting with an initiator methionine:
[OlOSJpVAX-PC-A: B-A-D-D-A-B-A-A
[0106]pVAX-PC-B: D-A-B-A-A-D-B-A
[0107)pVAX-PC-C: E-A-D-B-A-B-E-A-A
[0108]pVAX-BC-A: B-A-C-B-A-A-C-A
[0109)pVAX-BC-B: C-A-B-C-A-A-B-A
[0110] pVAX-BC-C: E-A-A-B-C-B-A-A
[0111] These arrays were inserted into the same vector backbone described in the examples above. The plasmid vectors were used to immunize mice essentially as described in Example 2 and the resulting CTL were tested for their ability to specifically lyse target cells pulsed with the peptide NY-ESO-1 157-165, corresponding to element B above. Both pVAX-PC-A and pVAX-BC-A were found to induce specific lytic activity. Comparing the contexts of the epitope (element B) in the various arrays, and particularly between pVAX-PC-A and pVAX-BC-A, between pVAX-PC-A and pVAX-PC-B, and between pVAX-BC-A and pVAX-BC-C, it was concluded that it was the first occurrence of the epitope in pVAX-PC-A and pVAX-BC-A that was being correctly processed and presented. In other words an initiator methionine followed by elements B-A constitute a substrate/liberation sequence for the presentation of element B. On this basis a new expression cassette for use as a vaccine was constructed encoding the following elements:
[0112] An initiator methionine, [0113] NY-ESO-1 ~ 57-165 (bold) - a housekeeping epitope, [0114] SSX24~-49 (italic) -providing appropriate context for processing, and [0115] NY-ESO-1 ~~_ ~ gp - to avoid "short sequence" problems and provide immune epitopes.
[0116) Thus the construct encodes the amino acid sequence:
[0117] M-SLLMWITQC-KASEKIFYV
RCGARGPESRLLEFYLAMPFATPMEAELARRSLAQDAPPLPVPGVLLKEFTVSGNIL,TIRLTA
ADHRQLQLSISSCLQQLSLLMWITQCFLPVFLAQPPSGQRR (SEQ ID NO. 17) and MSLLMWITQCKASEKIFYV (SEQ ID NO. 18) constitutes the liberation or substrate sequence. A
polynucleotide encoding SEQ ID NO. 17 (SEQ ID NO. 19: nucleotides 12-380) was inserted into the same plasmid backbone as used for pMA2M generating the plasmid pN157.
Example 4 [0118] A construct similar to pN157 containing the whole epitope array from pVAX-PC-A was also made and designated pBPL. Thus the encoded amino acid sequence in pBPL is:
[0119] M-SLLMWITQC-KASEKIFYY GLPSIPVHPI-GLPSIPVHPI-KASEKIFYV
SLLMWITQC-KASEKIFYV KASEKIFYV
RCGARGPESRLLEFYLAMPFATPMEAELARRSLAQDAPPLPVPGVLLKEFTVSGNIL,TIRLTA
ADHRQLQLSISSCLQQLSLLMWITQCFLPVFLAQPPSGQRR (SEQ m NO. 20).
[0120] SEQ LD NO. 21 is the polynucleotide encoding SEQ ID NO. 20 used in pBPL.
[0121] A portion of SEQ ID NO. 20, IKASEKIFYVSLLMWITQCKASEKIFYVK (SEQ
m NO. 22) was made as a synthetic peptide and subjected to in vitro proteasomal digestion analysis with human immunoproteasome, utilizing both mass spectrometry and N-terminal pool sequencing.
The identification of a cleavage after the C residue indicates that this segment of the construct can function as a substrate or liberation sequence for NY-ESO-1 ~5~_~65 (SEQ ID
NO. 12) epitope (see Figure 6). Figure 7 shows the differential processing of the SLLMWITQC epitope (SEQ ID NO. 12) in its native context where the cleavage following the C is more efficiently produced by housekeeping than immunoproteasome. The immunoproteasome also produces a major cleavage internal to the epitope, between the T and the Q when the epitope is in its native context, but not in the context of SEQ ID NO. 22 (compare fig. 6 and 7).
Example 5 [0122] Screening of further epitope arrays led to the identification of constructs promoting the expression of the epitope SSX-24_49 (SEQ ID NO. 13). In addition to some of the array elements defined in Example 3, the following additional elements were also used:
[0123) SSX-457-65:VMTKLGFKV (SEQ lD NO. 23) Array element F.
[0124] PSMA730-739 RQ~~TV (SEQ ID NO. 24) Array element G.
[0125] A construct, denoted CTLA02, encoding an initiator methionine and the.
array F-A-G-D-C-F-G-A, was found to successfully immunize HLA-A2 transgenic mice to generate a CTL
response recognizing the peptide SSX-241-49 (SEQ 117 NO. 13).
[0126] As described above, it can be desirable to combine a sequence with substrate or liberation sequence function with one that can be processed into immune epitopes. Thus SSX-2 ~ 5_ 183 (SEQ ~ NO. 25) was combined with all or part of the array as follows:
[0127] CTLS 1: F-A-G-D-C-F-G-A- SSX-2 ~ 5_ ~ g3 (SEQ 1D NO. 26) [0128] CTLS2: SSX-2 ~ 5_ ~ 83 - F-A-G-D-C-F-G-A (SEQ ID NO. 27) [0129] CTLS3: F-A-G-D- SSX-215-~ 83 (SEQ ID NO. 28) [0130] CTLS4: SSX-2~5_~g3 -C-F-G-A (SEQ ID NO. 29).
[0131] All of the constructs except CTLS3 were able to induce CTL recognizing the peptide SSX-24_49 (SEQ >D NO. 13). CTLS3 was the only one of these four constructs which did not include the second element A from CTLA02 suggesting that it was this second occurrence of the element that provided substrate or liberation sequence function. In CTLS2 and CTLS4.the A element is at the C-terminal end of the array, as in CTLA02. In CTLS1 the A element is immediately followed by the SSX-2 ~ 5_ ~ g3 segment which begins with an alanine, a residue often found after proteasomal cleavage sites (Toes, R.E.M., et al., J. Exp. Med. 194:1-12, 2001). SEQ )D NO. 30 is the polynucleotide sequence encoding SEQ ID NO. 26 used in CTLS I, also called pCBP.
(0132] A portion of CTLS1 (SEQ ID NO. 26), encompassing array elements F-A-SSX-215-23 with the sequence RQIYVAAFTV-KASEKIFYY AQIPEKIQK (SEQ ID NO. 31 ), was made as a synthetic peptide and subjected to in vitro proteasomal digestion analysis with human immunoproteasome, utilizing both mass spectrometry and N-terminal pool sequencing. The observation that the C-terminus of the SSX-241-49 epitope (SEQ ID NO. 13) was generated (see Figure 8) provided further evidence in support of substrate or liberation sequence function. The data in Figure 9 showed the differential processing of the SSX-24~-49 epitope, KASEKIFYh (SEQ >D NO.
13), in its native context, where the cleavage following the V was the predominant cleavage produced by housekeeping proteasome, while the immunoproteasome had several major cleavage sites elsewhere in the sequence. By moving this epitope into the context provided by SEQ >D NO. 31 the desired cleavage became a major one and its relative frequency compared to other immunoproteasome cleavages was increased (compare figs. 8 and 9). The data in figure 8B also showed the similarity in specificity of mouse and human immunoproteasome lending support to the usefulness of the transgenic mouse model to predict human antigen processing.
Example 6 [0133] Screening also revealed substrate or liberation sequence function for a tyrosinase epitope, Tyr2o~-215 (SEQ >D NO. 32), as part of an array consisting of the sequence [Tyre _ ~ 7- Tyr2o7-215]4~ ~MLLAVLYCLLWSFQTSA-FLPWHRLFL]4, (SEQ ID NO. 33). The same vector backbone described above was used to express this array. This array differs from those of the other examples in that the Tyr~_~7 segment, which was included as a source of immune epitopes, is used as a repeated element of the array. This is in contrast with the pattern shown in the other examples where sequence included as a source of immune epitopes and/or length occurred a single time at the beginning or end of the array, the remainder of which was made up of individual epitopes or shorter sequences.
Plasmid construction [0134] The polynucleotide encoding SEQ ID NO. 33 was generated by assembly of annealed synthetic oligonucleotides. Four pairs of complementary oligonucleotides were synthesized which span the entire coding sequence with cohesive ends of the restriction sites of Afl II and EcoR I
at either terminus. Each complementary pair of oligonucleotides were first annealed, the resultant DNA fragments were ligated stepwise, and the assembled DNA fragment was inserted into the same vector backbone described above pre-digested with Afl II/EcoR I. The construct was called CTLT2/pMEL and SEQ 117 NO. 34 is the polynucleotide sequence used to encode SEQ 117 NO. 33.
Example 7 Administration of a DNA ~lasmid formulation of a immunotherapeutic for melanoma to humans.
[0135] An MA2M melanoma vaccine with a sequence as described in Example 1 above, was formulated in 1 % Benzyl alcohol, I % ethyl alcohol, O.SmM EDTA, citrate-phosphate, pH 7.6.
Aliquots of 200, 400, and 600 pg DNA/ml were prepared for loading into MIhIIMED 407C infusion pumps. The catheter of a SILHOUETTE infusion set was placed into an inguinal lymph node visualized by ultrasound imaging. The pump and infusion set assembly was originally designed for the delivery of insulin to diabetics. The usual l7mm catheter was substituted with a 3lmm catheter for this application. The infizsion set was kept patent for 4 days (approximately 96 hours) with an infusion rate of about 25 pl/hour resulting in a total infused volume of approximately 2.4 ml. Thus the total administered dose per infusion was approximately 500, and 1000 pg;
and can be 1500 pg, respectively, for the three concentrations described above. Following an infusion, subjects were given a 10 day rest period before starting a subsequent infusion. Given the continued residency of plasmid DNA in the lymph node after administration and the usual kinetics of CTL response following disappearance of antigen, this schedule will be sufficient to maintain the immunologic CTL response.
Example 8 [0136] SEQ 1D NO. 22 is made as a synthetic peptide and packaged with a cationic lipid protein transfer reagent. The composition is infused directly into the inguinal lymph node (see example 7) at a rate of 200 to 600 pg of peptide per day for seven days, followed by seven days rest.
An initial treatment of 3-8 cycles are conducted.
Example 9 [0137) A fusion protein is made by adding SEQ )D NO. 34 to the 3' end of a nucleotide sequence encoding herpes simplex virus 1 VP22 (SEQ )D NO. 42) in an appropriate mammalian expression vector; the vector used above is suitable. The vector is used to transform HEK 293 cells and 48 to 72 hours later the cells are pelleted, lysed and a soluble extract prepared. The fusion protein is purified by affinity chromatagraphy using an anti-VP22 monoclonal antibody. The purified fusion protein is administered intranodally at a rate of 10 to 100 pg per day for seven days, followed by seven days rest. An initial treatment of 3-8 cycles are conducted.
[0138) Further, the present invention can utilize various aspects of the following: U.S.
Patent Application Nos. 09/380,534, filed on September 1, 1999, entitled A
METHOD OF
INDUCING A CTL RESPONSE; 09/776,232, filed on February 2, 2001, entitled METHOD OF
INDUCING A CTL RESPONSE; 09/715,835, filed on November 16, 2000, entitled AVOmANCE
OF UNDESIRABLE REPLICATION INTERMEDIATES IN PLASMID PROPOGATION;
09/999,186, filed on November 7, 2001, entitled METHODS OF COMMERCIALIZING AN
ANTIGEN; and Provisional U.S. Patent Application No 60/274,063, filed on March 7, 2001, entitled ANTI-NEOVASCULAR VACCINES FOR CANCER.
Table 11 Partial listine of SEO ID NOS.
1 ELAGIGILTV melan-A 26-35 A27L
2 Melan -A rotein Accession number: NP
3 T osinase rotein Accession number: P14679 4 MLLAVLYCLELAGIGILTVYMDGTMSQVGILT pMA2M expression product VILGVLLLIGCWYCRRRNGYRALMDKSLHVG
TQCALTRRCPQEGFDHRDSKVSLQEKNCEPV
MLLAVLYCLELAGIGILTVYMDGTMSQV Liberation or substrate sequence for SEQ m NO. 1 from MA2M
6 MLLAVLYCL t osinase 1-9 7 YMDGTMSQV ' t osinase 369-377 8 EAAGIGILTV melan-A 26-35 cttaagccaccatgttactagctgttttgtactgcctggaactpM~M insert agcagggatcggcatattgacagtgtatatgga tggaacaatgtcccaggtaggaattctgacagtgatcctggga gtcttactgctcatcggctgttggtattgtaga agacgaaatggatacagagccttgatggataaaagtcttcatg ttggcactcaatgtgccttaacaagaagatgcc cacaagaagggtttgatcatcgggacagcaaagtgtctcttca agagaaaaactgtgaacctgtgtagtgagcggc cgc MVLYCLELAGIGILTVYMDGTAVLYCLELAGI Epitope array from pVAXM2 ~ and _77_ GILTVYMDGTMLAVLYCLELAGIGILTVYMD pVAXMI
GTMSLLAVLYCLELAGIGILTV
11 NY-ESO-1 rotein Accession number: P78358 16 AVLYCL t rosinase 4-9 17 MSLLMWITQCKASEKIFYVRCGARGPESRLLE pN157 expression product FYLAMPFATPMEAELARRSLAQDAPPLPVPGV
LLKEFTV SGNILTIRLTAADHRQLQLSISSCLQ
LSLLMWITQCFLPVFLA PPSGQRR
18 MSLLMWITQCKASEKIFYV liberation or substrate sequence for SE ID NO. 12 from N157 19 cttaagccaccatgtccctgttgatgtggatcacgcagtgcaa~ge~ fOrpN157 agcttcggagaaaatcttctacgtacggtgcgg tgccagggggccggagagccgcctgcttgagttctacctcgcc atgcctttcgcgacacccatggaagcagagctg gcccgcaggagcctggcccaggatgccccaccgcttcccgtgc caggggtgcttctgaaggagttcactgtgtccg gcaacatactgactatccgactgactgctgcagaccaccgcca actgcagctctccatcagctcctgtctccagca gctttccctgttgatgtggatcacgcagtgctttctgcccgtg tttttggctcagcctccctcagggcagaggcgc tagtgagaattc 20 MSLLMWITQCKASEKIFYVGLPSIPVHPIGLPSIpBPL expression product PVHPIKASEKIFYVSLLMWITQCKASEKIFYVK
ASEKIFYVRCGARGPESRLLEFYLAMPFATPM
EAELARRSLAQDAPPLPVPGVLLKEFTVSGNIL, TIRL,TAADHRQLQLSISSCLQQLSLLMWITQCF
LPVFLA PPSGQRR
21 atgtccctgttgatgtggatcacgcagtgcaaagcttcggagap$PLInSertCOdlngreglOri aaatcttctatgtgggtcttccaagtattcctg ttcatccaattggtcttccaagtattcctgttcatccaattaa agcttcggagaaaatcttctatgtgtccctgtt gatgtggatcacgcagtgcaaagcttcggagaaaatcttctat gtgaaagcttcggagaaaatcttctacgtacgg tgcggtgccagggggccggagagccgcctgcttgagttctacc tcgccatgcctttcgcgacacccatggaagcag agctggcccgcaggagcctggcccaggatgccccaccgcttcc cgtgccaggggtgcttctgaaggagttcactgt gtccggcaacatactgactatccgactgactgctgcagaccac cgccaactgcagctctccatcagctcctgtctc cagcagctttccctgttgatgtggatcacgcagtgctttctgc ccgtgtttttggctcagcctccctcagggcaga ggcgctagtga 22 IKASEKIFYVSLLMWITQCKASEKIFYVK Substrate in Fig. 6 23 VMTKLGFKV SSX-457_65 24 RQIYVAAFTV PSMA73o-739 25 AQIPEKIQKAFDDIAKYFSKEEWEKMKASEKIFSSX-2 ~ 5_t g3 YVYMKRKYEAMTKLGFKATLPPFMCNKRAE
DFQGNDLDNDPNRGNQVERPQMTFGRLQGIS
PKIMPKKPAEEGNDSEEVPEASGPQNDGKELC
PPGKPTTSEKIHERSGPKRGEHAWTHRLRERK
LVIYEEISDP
_78_ 26 MVMTKLGFKVKASEKIFYVRQIYVAAFTV CTLS1/pCBPexpressionproduct GLPSIPVHPITQCFLPVFLVMTKLGFKVRQIYV
AAFTVKASEKIFYVAQIPEKIQKAFDDIAKYFS
KEEWEKMKASEKIFYVYMKRKYEAMTKLGF
KATLPPFMCNKRAEDFQGNDLDNDPNRGNQ
VERPQMTFGRLQGISPKIMPKKPAEEGNDSEE
VPEASGPQNDGKELCPPGKPTTSEKIHERSGPK
RGEHA W THRLRERKQLV IYEEISDP
27 MAQIPEKIQKAFDDIAKYFSKEEWEKMKASE CTLS2 expression product KIFYVYMKRKYEAMTKLGFKATLPPFMCNKR
AEDFQGNDLDNDPNRGNQVERPQMTFGRLQ
GISPKIMPKKPAEEGNDSEEVPEASGPQNDGK
ELCPPGKPTTSEKIHERSGPKRGEHAWTHRLR
ERKQLVIYEEISDPVMTKLGFKVKASEKIFYV
RQIYVAAFTVGLPSIPVHPITQCFLPVFLVMTK
LGFKVRQIYVAAFTVKASEKIFYV
28 MVMTKLGFKVKASEKIFYVRQIYVAAFTV CTLS3 expression product GLPSIPVHPIAQIPEKIQKAFDDIAKYFSKEEWE
KMKASEKIFYV YMKRKYEAMTKLGFKATLPP
FMCNKRAEDFQGNDLDNDPNRGNQVERPQM
TFGRLQGISPKIMPKKPAEEGNDSEEVPEASGP
QNDGKELCPPGKPTTSEKIHERSGPKRGEHAW
THRLRERK LVIYEEISDP
29 MAQIPEKIQKAFDDIAKYFSKEEWEKMKASE CTLS4 expressipn product KIFYV YMKRKYEAMTKLGFKATLPPFMCNKR
AEDFQGNDLDNDPNRGNQVERPQMTFGRLQ
GISPKIMPKKPAEEGNDSEEVPEASGPQNDGK
ELCPPGKPTTSEKIHERSGPKRGEHAWTHRLR
ERKQLVIYEEISDPTQCFLPVFLVMTKLGFKVR
QIYVAAFTVKASEKIFYV
30 atggtcatgactaaactaggtttcaaggtcaaagcttcggagapCBP Insert COdlrig region aaatcttctatgtgagacagatttatgttgcag ccttcacagtgggtcttccaagtattcctgttcatccaattac gcagtgctttctgcccgtgtttttggtcatgac taaactaggtttcaaggtcagacagatttatgttgcagccttc acagtgaaagcttcggagaaaatcttctacgta gctcaaataccagagaagatccaaaaggccttcgatgatattg ccaaatacttctctaaggaagagtgggaaaaga tgaaagcctcggagaaaatcttctatgtgtatatgaagagaaa gtatgaggctatgactaaactaggtttcaaggc caccctcccacctttcatgtgtaataaacgggccgaagacttc caggggaatgatttggataatgaccctaaccgt gggaatcaggttgaacgtcctcagatgactttcggcaggctcc agggaatctccccgaagatcatgcccaagaagc cagcagaggaaggaaatgattcggaggaagtgccagaagcatc tggcccacaaaatgatgggaaagagctgtgccc cccgggaaaaccaactacctctgagaagattcacgagagatct ggacccaaaaggggggaacatgcctggacccac agactgcgtgagagaaaacagctggtgatttatgaagagatca gcgacccttagtga 31 RQIYVAAFTVKASEKIFYVAQIPEKIQK Fig. 8 substrate/ CTLS1-2 32 FLPWIIRLFL T~2o7-2~5 33 MLLAVLYCLLWSFQTSAFLPWHRLFLMLLAV CTLT2/pMEL expression product LYCLLWSF TSAFLPWHRLFLMLLAVLYCLL
WSFQTSAFLPWHRLFLMLLAVLYCLLWSFQT
SAFLP WHRLFL
SE . ID N0.:351 Influenza NSI 122-130 AIMDKNIIL HLA-A*0201 SE . ID N0.:352 Influenza NSI 123-132 IMDKNIILKA HLA-A*0201 A
SE . ID N0.:353 Influenza NP 383-391 SRYWAIRTR HLA-B*2705 A
SEQ. ID N0.:354 Influenza NP 147-155 TY RTRALV H2-Kd A
SEQ. ID N0.:355 Influenza HA 210-219 TYVSVSTSTL H2-Kd A
SE . ID N0.:356 Influenza HA 518-526 IYSTVASSL H2-Kd A
SE . ID N0.:357 Influenza HA 259-266 FEANGNLI H2-Kk A
SEQ. ID N0.:358 Influenza HA 10-18 IEGGWTGMI H2-Kk A
SE . ID N0.:359) Influenza NP 50-57 SDYEGRLI H2-Kk A
(SEQ. ID N0.:360) Influenza NSI 152-160 EEGAIVGEI H2-Kk a SEQ. LD N0.:361 Influenza NP 336-374 ASNENMETM H2Db SE .117 N0.:362 Influenza NP 366-374 ASNENMDAM H2Db SEQ. ID N0.:363 Influenza NP 85-94 KLGEFYN MM HLA-A*0201 B
SEQ. ID N0.:364 Influenza NP 85-94 KAGEFYNQMM HLA-A*0201 B
SEQ. ID N0.:365 Influenza HA 204-212 LYQNVGTYV H2Kd JAP
SE . ID N0.:366 Influenza HA 210-219 TYVSVGTSTL H2-Kd JAP
(SEQ. ID N0.:367 Influenza HA 523-531 VYQILATYA H2-Kd JAP
SE . ID N0.:368 Influenza HA 529-537 IYATVAGSL H2-Kd JAP
SE . ID N0.:369 Influenza HA 210-219 TYVSVGTSTI L>I H2-Kd JAP
SE . ID N0.:370 Influenza HA . 255-262 FESTGNLI H2-Kk JAP
SE . ID N0.:371 JHMV cA 318-326 APTAGAFFF H2-Ld SE . ID N0.:372 LCMV NP 118-126 RP ASGVYM H2-Ld SE .117 N0.:373 LCMV NP 396-404 F P NGQFI H2-Db SEQ. ID N0.:374 LCMV GP 276-286 SGVENPGGYCL H2-Db (SEQ. ID N0.:375 LCMV GP 33-42 KAVYNFATCG H2-Db (SEQ. ID N0.:376 MCMV 89 168-176 YPHFMPTNL H2-Ld SE . >D N0.:377 MHV spike 510-518 CLSWNGPHL H2-Db rotein SE . ID N0.:378 MMTV env 36 474-482 SFAVATTAL H2-Kd SEQ. D7 N0.:379 MMTV a 27 425-433 SYETFISRL H2-Kd SE . ID N0.:380 MMTV env 73 544-551 ANYDFICV H2-Kb (SEQ. ID N0.:381 MuLV env 15E 574-581 KSPWFTTL H2-Kb SEQ. ID N0.:382 MuLV env gp70189-196 SSWDFITV H2-Kb SE . ID N0.:383 MuLV a 75K 75-83 CCLCLTVFL H2-Db (SE .117 N0.:384 MuLV env 70 423-431 SPSYVYHQF H2Ld SE . ID N0.:385 MV F rotein437-447 SRRYPDAVYLH HLA-B*2705 (SEQ. ID N0.:386 My F rotein438-446 RRYPDAVYL HLA-B*2705 Virus Protein AA T cell epitope MHC MHC molecule Position ligand Anti en (SE . ID N0.:387 My NP 281-289 YPALGLHEF H2-Ld (SE . ID N0.:388 My HA 343-351 DPV117RLYL H2-Ld SE . ID N0.:389 MV HA 544-552 SPGRSFSYF H2-Ld (SEQ. ID N0.:390 Poliovirus VP1 111-118 TYKDTV L H2-kd SE . ID N0.:391 Poliovirus VP1 208-217 FYDGFSKVPL H2-Kd SE . ID N0.:392 Pseudorabies6111 455-463 IAGIGILAI HLA-A*0201 virus SE . ID N0.:393 RabiesvirusNS 197-205 VEAEIAHQI H2-Kk SEQ. ID N0.:394 Rotavirus VP7 33-40 11YRFLL1 H2-Kb SE . ID N0.:395) Rotavirus VP6 376-384 VGPVFPPGM H2-Kb SE . ID N0.:396 Rotavirus VP3 585-593 YSGYIFRDL H2-Kb SE .117 N0.:397 RSV M2 82-90 SYIGSINNI H2-Kd SEQ. ID N0.:398 SN a 11 C 179-190 EGCTPYDTNQML Mamu-A*O1 SE . )17 N0.:399 SV NP 324-332 FAPGNYPAL H2-Db SEQ. ID N0.:400 SV NP 324-332 FAPCTNYPAL H2-Kb SE . ID N0.:401 SV40 T 404-411 VVYDFLKC H2-Kb SE . ID N0.:402) SV40 T 206-215 SAINNYA KL H2-Db SE . ID N0.:403 SV40 T 223-231 CKGVNKEYL H2-Db SE . ID N0.:404 SV40 T 489-497 GINNLDNL H2-Db SEQ. ID N0.:405 SV40 T 492-S00 NNLDNLRDY(L) H2-Db SEQ. ID N0.:406 SV40 T 560-568 SEFLLEKRI H2-Kk SEQ. ID N0.:407 VSV NP 52-59 RGYVY GL H2-Kb SEQ. ID N0.:408 Table 2 IEILA-A1 Position Anti en Source T cell a EADPTGHSY MAGE-1 161-169 ito es SEQ. ID N0.:409 VSDGGPNLY Influenza A PB 1591-599 SEQ. ID N0.:410 CTELKLSDY Influenza A NP 44-52 SEQ. ID N0.:411 SEQ. ff~ N0.:412 HLA-A201 MLLSVPLLLG Calreticulin si al se uence SEQ, )D N0.:413 SE . >D N0.:414 YMDGTMS V Tyrosinase 369-377 SE . ID N0.:415 SEQ. ID N0.:416 LLGFVFTLTV Influenza MP 59-68 SEQ. ID N0.:417 LLFGYPVYVV HTLV-1 tax 11-19 (SEQ. )D N0.:418 GLSPTVWLSV HBV sA 348-357 SEQ.117 N0.:419 WLSLLVPFV HBV sA 335-343 SE . ID N0.:420 FLPSDFFPSV HBV cA 18-27 SEQ. ID N0.:421) SEQ. ID N0.:422) (SEQ. )D N0.:423 KLGEFYNQMM Influenza BNP 85-94 SEQ. m N0.:424) SE . ID N0.:425) SE . ID N0.:426) (SE . )D N0.:427 MLLAVLYCL T rosinase 1-9 SE . II7 N0.:428) AAGIGILTV Melan A~IVIart-127-35 (SEQ. ID N0.:429 YLEPGPVTA Pmel 17/ 100 480-488 SEQ. ID N0.:430 ~ ILDGTATLRL Pmel 17/ gp 100 457-466 SE . ID N0.:431) LLDGTATLRL Pmel 100 457-466 SE . ID N0.:432 ITD VPFSV Pmel 100 209-217 SE . ID N0.:433 KTWGQYWQV Pmel 100 154-162 SE . ID N0.:434) TITDQVPFSV Pmel 100 208-217 SE . ID N0.:435) AFHIIVAREL HIV- I nef 190-198 SE . ID N0.:436) YLNKIQNSL P. falci arum CSP 334-342 SE . ID N0.:437 MMRKLAILSV P. falci arum CSP 1 -10 SE . ID N0.:438 KAGEFYN MM Influenza BNP 85-94 SE . ID N0.:439) SEQ. ID N0.:440) SE . ID N0.:441 SE . ID N0.:442) SE . ID N0.:443 SE . ID N0.:444) SEQ. ID N0.:445) SE . ID N0.:446) SE . ID N0.:447 SE . ID N0.:448 SE . ID N0.:449) SEQ. >D N0.:450 SE .117 N0.:451 SEQ.117 N0.:452) SE . ID N0.:453 SE . ID N0.:454 SE . ID N0.:455 SE . ID N0.:456 SE . ID N0.:457 SE . ID N0.:458 SEQ, ID N0.:459 SE . ID N0.:460 SE . ID N0.:461 SE . ID N0.:462 SE . ID N0.:463 SE . ID N0.:464 AIMDKNIIL Influenza A NS1 122-130 SE . ID N0.:465 IMDKNIILKA Influenza A NSl 123-132 SE . ID N0.:466 SE . ID N0.:467 SE . ID N0.:468 LRRHIDLLV HCV env E 66-75 SEQ, ID N0.:469 DLCGSVFLV HCV env E 88-96 SEQ. ID N0.:470 SMVGNWAKV HCV env E 172-180 SE . ID N0.:471 SE . ID N0.:472 SEQ. ID N0.:473 SEQ. ID N0.:474 SE .117 N0.:475 LLAPGAK NV HCV NSl 19-28 SE . ID N0.:476 SE . ID N0.:477 SE .117 N0.:478 SEQ. >D N0.:479 SE . 117 N0.:480 SE . >D N0.:481 (SE . ID N0.:482 SE . ID N0.:483 VLYRYGSFSV Pmel 100 476-485 SE . >D N0.:484 YIGEVLVSV Non-filament forming class I myosin family (HA-2)**
(SE . ID N0.:485 SE . ID N0.:486 LLVPFV WFW HBV env 338-347 SE . ID N0.:487 SE . ID N0.:488 (SE . ID N0.:489 (SEQ. )D N0.:490 YLLPRRGPRL HCV core rotein 34-43 SE . ID N0.:491 LLPIFFCLWV HBV env 378-387 SE . ID N0.:492 YMDDVVLGA HBV Pol 538-546 SE . ID N0.:493 SE . ID N0.:494 (SEQ. ID N0.:495 SE . ID N0.:496 SE . ID N0.:497 SE . )D N0.:498 VMNILL YVV Glutarnic acid decarbox lase 114-123 SE . >D N0.:499 ILTVILGVL Melan A/Mart- 32-40 SE . ID NO.:500 SE . >D NO.:501 SE . ID N0.:502 IL,DSFDPLV HCV NSS 239-247 SE . ID N0.:503 LLLCLIFLL HBV env 250-258 (SEQ. m N0.:504 LIDYQGMLPV HBV env 260-269 SEQ. ID N0.:505 SIVSPFIPLL HBV env 370-379 SE . ID N0.:506 FLLTRILTI HBV env 183-191 (SE . ID N0.:507 HLGNVKYLV P. faci arum TRAP 3-11 SE . ID N0.:508 GIAGGLALL P. faci arum TRAP 500-508 SE . ID N0.:509 SEQ.117 N0.:510 SE .117 N0.:511 (SEQ. ID N0.:512 SEQ. ID N0.:513) VLPDVFIRCV N-acetylglucosaminyltransferase V
Gnt-V intron SEQ. ID N0.:514 VLPDVFIRC N-acetylglucosaminyltransferase V
Gnt-V intron SEQ. ID N0.:515 AVGIGIAVV Human CD9 SEQ. ID N0.:516 LVVLGLLAV Human lutam ltransferase SE . ID N0.:517 ALGLGLLPV Human G rotein cou led rece for (SEQ. ID N0.:518) SEQ. ID N0.:519 SE .117 N0.:520 IAGIGILAI Pseudorabies GIN 455-463 SEQ.117 N0.:521 LIVIGILIL Adenovirus 3 E3 9kD 30-38 SEQ. ID N0.:522 LAGIGLIAA S. Lincolnensis ImrA
SE . ID N0.:523 VDGIGILTI Yeast sa-177-85 SEQ. ID N0.:524 GAGIGVLTA B. polymyxa, [3cndoxylanase (SEQ. ll7 N0.:525) AAGIGII I E. coli methionine s thane SEQ. ID N0.:526 AGIGILLA E. coli h othetical rotein SEQ. ID N0.:527 KARDPHSGHFV CDK4wl 22.32 SEQ. ID N0.:528 SEQ. ID N0.:529 SEQ. ID N0.:530 SLYNTVATL HIV- I a 17 77-85 SEQ. ID N0.:531 ELVSEFSRV HER-2, m>V substituted SE . ID N0.:532 SEQ. ID N0.:533 SEQ. ID N0.:534 SEQ. ID N0.:535 GLHCYEQLV HPV 6b E7 21-30 SEQ. ID N0.:536 PLKQHFQIV HPV 6b E7 47-55 SE . ID N0.:537 SE . >I7 N0.:538 AIMEKNIML Influenza Alaska NS 1 122-130 SEQ. ID N0.:539 YLKTI NSL P. falci arum c 36 CSP
SEQ. ID N0.:540 YLNKIQNSL P. falci arum c 39 CSP
SEQ. ID N0.:541 YMLDL PETT HPV 16 E7 11-20*
SE .117 N0.:542 LLMGTLGIV HPV16 E7 82-90**
SE . ID N0.:543 SEQ. ID N0.:544 SE . ID N0.:545 SEQ. ID N0.:546 TIH>DIIL,EC HPV 16 E6 29-37 SEQ. ID N0.:547 SE . ID N0.:548) VIL,GVLLLI Melan A/Mart-1 35-43 SE . ID N0.:549 ALMDKSLHV Melan A/Mart- 1 56-64 SE . ID N0.:550 GIL,TVILGV Melan A/Mart- 1 31-39 SE . ID NO.:551 T cell a ito MINAYLDKL P. Falci arum STARP 523-531 es SE . ID N0.:552) AAGIGILTV Melan A/Mart- 127-35 SE . ID N0.:553 FLPSDFFPSV HBV cA 18-27 SE . ID N0.:554 Motif unknownSVRDRLARL EBNA-3 464-472 T cell a ito SE . ID NO.:555 es T cell a ito AAGIGILTV Melan A/Mart-1 27-35 es SE . ID N0.:556 FAYDGKDYI Human MHC I-of 140-148 SE . )D N0.:557 T cell a ito AAGIGILTV Melan A/Mart-1 27-35 es SE . ID N0.:558 FLPSDFFPSV HBV cA 18-27 SE . ID N0.:559 Motif unknownAAGIGILTV Meland A/Mart-1 27-35 T cell a ito SE . ID N0.:560 es FLPSDFFPSV HBV cA 18-27 SEQ. ID N0.:561 AAGIGILTV Melan A/Mart-1 27-35 SE . ID N0.:562 ALLAVGATK Pmel17 100 17-25 SE . ID N0.:563 T cell a ito R L R D L L L I V HIV-1 41 768-778 es T R
SE . ID N0.:564 VPLRPMTYK HIV-1 nef 73-82 SEQ. ID N0.:565) SE . ID N0.:566) RLRPGGKKK HIV- 1 a 17 20-29 SE . ID N0.:567 ILRGSVAHK Influenza NP 265-273 SE . ID N0.:568 SEQ. ID N0.:569 SE .117 N0.:570 SE . ID N0.:571 SE . ID N0.:572 Motif unknownKIFSEVTLK Unknown; muta melanoma peptide ted I83L 1?5-183 T cell a SEQ. ID N0.:573 ito a YVNVNMGLK* HBV cA 88-96 (SE . ID N0.:574 T cell a IVTDFSVIK EBNA-4 416-424 ito es SEQ. 117 N0.:575) SEQ. ID N0.:576) (SE . ID N0.:577 AIF SSMTK HIV- I a 24 325-333 SE .117 N0.:578) QVPLRPMTYK HIV-1 nef 73-82 SE . ID N0.:579 SE . ID N0.:580) AAVDLSHFLKEK HIV-1 nef 83-94 (SE . ID N0.:581 K
SE . ID N0.:581 HLA-A24 S Y L D S G I H F* ~3-catenin, mutated (proto-onocogen) SE . 117 N0.:582 T cell a RYLKDQQLL HIV GP 41 583-591 ito es SE . ID N0.:583) AYGLDFYIL, P15 melanoma A 10- 18 SE . ID N0.:584) AFLPWHRLFL T osinase 206-215 SE . ID N0.:585) AFLPWHRLF Tyrosinase 206-214 SE . ID N0.:586 RYSIFFDY Ebna-3 246-253 SE . ID N0.:587 T cell a ETINEEAAEW HIV- 1 a 24 203-212 ito a SE . ID N0.:588 T cell a STLPETTVVRR HBV cA 141 -151 ito es SE . ID N0.:589 MSL R FLR ORF 3P- 75 294-321 b SE . ID N0.:590 LLPGGRPYR TRP t osinase rel. 197-205 SE . ID N0.:591 T cell a IVGLNKIVR HIV a 24 267-267-275 ito a SE . ID N0.:592 AAGIGILTV Melan A/Mart- 127 35 SE . ID N0.:593 Table 3 sets forth additional antigens useful in the invention that are available from the Ludwig Cancer Institute. The Table refers to patents in which the identified antigens can be found.
TRA refers to the tumor-related antigen and the LUD No. refers to the Ludwig Institute number.
Table 3 TRA LUD Patent Date Patent Peptide (Antigen) HLA
No. No. Issued MAGE-4 5293 5,405,94011 April EVDPASNTY HLA-AI
(SEQ. ID N0.:532) MAGE-41 5293 5,405,94011 April EVDPTSNTY HLA-A
(SEQ ID N0:533) MAGE-5 5293 5,405,94011 April EADPTSNTY HLA-A
(SEQ ID N0:534) MAGE-51 5293 5,405,9401 1 April EADPTSNTY HLA-A
(SEQ ID N0:534) MAGE-6 5294 5,405,940I 1 April EVDPIGHVY HLA-AI
(SEQ ID N0:535) 5299.25,487,97430 January MLLAVLYCLL HLA-A2 (SEQ ID N0:536) 5360 5,530,09625 June 1996MLLAVLYCL HLA-B44 (SEQ ID N0:537) Tyrosinase5360.15,519,11721 May 1996 SEIWRDIDFA HLA-B44 (SEQ ID N0:538) SEIWRDIDF
(SEQ ID N0:539) Tyrosinase5431 5,774,31628 April XEIWRDIDF HLA-B44 (SEQ ID N0:540) MAGE-2 5340 5,554,72410 SeptemberSTLVEVTLGEV HLA-A2 (SEQ ID N0:541) LVEVTLGEV
(SEQ ID N0:542) V IFSKASEYL
(SEQ ID N0:543) IIVLAIIAI
(SEQ ID N0:544) (Continued) KIWEELSMLEV
(SEQ ID N0:545) TRA LUD Patent Date Patent Peptide (Antigen) HLA
No. No. Issued LIETSYVKV
(SEQ ID N0:546) 5327 5,585,46117 December FLWGPRALV HLA-A2 (SEQ ID NO: 547) TLVEVTLGEV
(SEQ ID N0:548) ALV ETSYV KV
(SEQ ID N0:549) MAGE-3 5344 5,554,50610 SeptemberK(WEELSVL HLA-A2 (SEQ ID N0:550) MAGE-3 5393 5,405,94011 April EVDPIGHLY HLA-Al (SEQ ID N0:551) MAGE 5293 5,405,94011 April EXDXSY HLA-Al (SEQ. ID N0.:552) (but not EADPTGHSY) (SEQ. ID N0.:553) E (A/V) D X5 Y
(SEQ. ID N0.:554) E(A/V)DPX4Y
(SEQ. ID N0.:555) E (A/V) D P (1/A/T) (SEQ. ID N0.:556) E (A/V) D P (I/A/T) (G/S) X2 Y
(SEQ. ID N0.:557) E (A/V) D P (1/A/T) (G/S) (H/N) X Y
E (A/V) DP (I/A/T) (G/S) (H/N) (L/T/V) Y
(SEQ. I I) N0.:559) MACE-I 5361 5,558.99524 SeptemberELHSAYGEPRKLLTQD HLA-C
(SEQ ID N0:560) Clone EHSAYGEPRKLL
(SEQ ID N0:561 ) SAYGEPRKL
(SEQ ID N0:562) MAGE-1 5253.4TBA TBA EADPTGHSY HLA-A
I
(SEQ ID N0:563) TRA LUD Patent Date Patent Peptide (Antigen) HLA
No. No. Issued BAGS 5310.1TBA TBA MAARAVFLALSAQLLQARLMKEHLA-C
(SEQ ID N0:564) Clone MAARAVFLALSAQLLQ HLA-C
(SEQ ID N0:565) Clone AARAVFLAL HLA-C
(SEQ ID N0:566) Clone GAGE 5323.25,648,22615 July 1997YRPRPRRY HLA-CW6 (SEQ. ID N0.:567) Table 4 Source Protein AA MHC T cell epitope Ref.
PositionmoleculesMHC
li and Anti en syntheticsyntheticsyntheticHLA-A2 ALFAAAAAV Parker, et peptides peptidespeptides al., - "Scheme for ranking potential HLA-A2 binding peptides based onindependent binding of individual peptide side-chains,"
J.
Immunol.
152:163-175 " GIFGGVGGV "
" GLDKGGGV "
" GLFGGFGGV "
" GLFGGGAGV "
" GLFGGGEGV "
" GLFGGGFGV "
" GLFGGGGGL "
" GLFGGGGGV "
" GLFGGGVGV "
" GLFGGVGGV "
" GLFGGVGKV "
" GLFKGVGGV "
" GLGGGGFGV "
" GLLGGGVGV "
" GLYGGGGGV "
" GMFGGGGGV "
" GMFGGVGGV "
" GQFGGVGGV "
" GVFGGVGGV "
" KLFGGGGGV "
" KLFGGVGGV "
" AILGFVFTL "
" GAIGFVFTL "
" GALGFVFTL "
" GELGFVFTL "
" GIAGFVFTL "
" GIEGFVFTL "
" GILAFVFTL "
" GILGAVFTL "
" GILGEVFTL "
" GILFGAFTL "
" GILGFEFTL "
" GILGFKFTL "
" GILGFVATL "
" GILGFVETL "
" GILGFVFAL "
" GIL,GFVFEL "
" GILGFVFKL "
" GILGFVFTA "
" GILGFVFTL "
" GILGFVFVL "
" GILGFVKTL "
" GILGKVFTL "
" GILKFVFTL "
" GILPFVFTL "
" GIVGFVFTL "
" GKLGFVFTL "
" GLLGFVFTL "
" G LGFVFTL "
" KALGFVFTL "
" KILGFVFTL "
" KILGKVFTL "
" AILLGVFML "
" AlYKRWIIL "
" ALFFFDIDL "
" ATVELLSEL "
" CLFGYPVYV "
" FIFPNYTIV "
" IISLWDS L "
" ILASLFAAV "
" ILESLFAAV "
" KLGEFFN M "
" KLGEFYN M "
" LLFGYPVYV "
" LLWKGEGAV "
" LMFGYPVYV "
" LNFGYPVYV "
" LQFGYPVYV "
" NIVAHTFKV "
" NLPMVATV "
" QMLLAIARL "
" QMWQARLTV "
" RLLQTGIHV "
" RLVNGSLAL "
" SLYNTVATL "
" TLNAWVKVV "
" WLYRETCNL j " YLFKRMIDL "
" GAFGGVGGV "
" GAFGGVGGY "
" GEFGGVGGV "
" GGFGGVGGV "
" GIFGGGGGV "
" GIGGFGGGL "
" GIGGGGGGL "
" GLDGGGGGV "
" GLDGKGGGV "
" GLDKKGGGV "
" GLFGGGFGF "
" GLFGGGFGG "
" GLFGGGFGN "
" GLFGGGFGS "
" GLFGGGGGI "
" GLFGGGGGM "
" GLFGGGGGT "
" GLFGGGGGY "
" GLGFGGGGV "
" GLGGFGGGV "
" GLGGGFGGV "
" GLGGGGGFV "
" GLGGGGGGY "
" GLGGGVGGV "
" GLLGGGGGV "
" GLPGGGGGV "
" GNFGGVGGV "
" GSFGGVGGV "
" GTFGGVGGV "
" AGNSAYEYV "
" GLFPGQFAY "
" HILLGVFML "
" ILESLFRAV "
" KKKYKLKHI "
" MLASIDLKY "
" MLERELVRK "
" KLFGFVFTV "
" ILDKKVEKV "
" ILKEPVHGV "
" ALFAAAAAY "
" GIGFGGGGL "
" GKFGGVGGV "
" GLFGGGGGK "
" EILGFVFTL "
" GIKGFVFTL "
" GQLGFVFTK I "
" ILGFVFTLT "
" KII,GFVFTK "
" KKLGFVFTL "
" KLFEKVYNY "
" LRFGYPVYV "
Human HSP60 140-148 HLA-B27 IRRGVMLAV Rammensee et al. I 997 " " 369-377 " KRI EIIEQ "
" " 469-477 " KRTLKIPAM "
YersiniaHSP60 35-43 " GRNVVLDKS "
" " 117-125 " KRGIDKAVI "
" " 420-428 " IRAASAITA "
" HSP 60 284-292 HLA- RRKAMFEDI 169 B*2705 P.falci LSA-1 1850-1857HLA-B3501KPKDELDY 170 arum Influenza 379-387 HLA- LELRSRYWA 183 NP B *4402 Tum-P35B 4-13 HLA-Dd GPPHSNNFGY 230 RotavirusVP7 33-40 IIYRFLLI 262 OGDH 104-112 H2-Ld QLSPYPFDL 253 TRP-2 181-188 p287 VYDFFVWL 284 DEAD box 547-554 p287 SNFVFAGI 283 Vector p287 SVVEFSSL 260 "artefact"
Epiope p287 AHYLFRNL 278 mimic of tumor A
" THYLFRNL "
Epitope " LNIYNTL 279 mimic of H-3 miHA
"
" LIYEFNTL "
" IPYIYNTL "
" IIYII'IIRL "
" LIYIFNTL "
HBV cA 93-100 " MGLKFR L 280 Human autoantigen51-58 " 1MIKFRNRL 281 LA
Mouse UTY H2Db WMHIINMDLI 303 rotein Mouse 53 232-240 " KYMCNSSCM 302 MURINE MDM2 441-449 " GRPKNGCIV 277 Epitope " AQHPNAELL 278 mimic of natural MuLV 75-83 " CCLCLTVFL 301 gag75K
P. CSP 375-383 p290 YENDIEKK 315 Falci arum " " 371-379 " DELDYENDI 315 HIV -1RT 206-214 " TEMEKEGKI 316 Rabies NS 197-205 VEAEIAH I 309, 310 InfluenzaNS1 152-160 " EEGANGEI 304 A
Murine SMCY 291 TENSGKDI 317 MHC class3-11 p293 AMAPRTLLL 318 1 leader NDlal 1-12 293 FFINILTLLVP 323 ha ND Beta 1-12 293 FFINIZTLLVP 323 ND al 1-17 " FFINILTLLVPILIAM324 ha ND Beta 1-17 " FFINALTLLVPILIAM"
COI 1-6 " FINRW 325 mitochondri al L. LemA 1-6 " IGWII 326 monocytoge nes SN gag 179-190 Mamu-A*O1EGCTPYDINQML 334 5,554,506 " IMPKAGLLI "
" KIWEELSVL "
" ALVETSYVKV "
" ThrLeuValGluValThrL"
euGl GIuVaI
" AlaLeuSerArgLysValA"
laGIuLeu " IleMetProLysAlaGIyLe"
uLeuIle " LysIleTrpGluGluLeuSe"
rValLeu " AlaLeuVaIGIuThrSerT"
yrValLysVa1 peptides HLA-A2 Lys Gly Ile 5,989,565 Leu Gly which Phe Val Phe bind Thr Leu to MHCs Thr Val " Gly Ile Ile "
Gly Phe Val Phe Thr Ile " Gly Ile Ile "
Gly Phe Val Phe Thr Leu " Gly Ile Leu "
Gly Phe Val Phe Thr Leu " Gly Leu Leu "
Gly Phe Val Phe Thr Leu " XXTVXXGVX, "
X=Leu or Ile " Ile Leu Thr "
Val Ile Leu Gl Val Leu " Tyr Leu Glu "
Pro Gly Pro Val Thr Ala " Gln Val Pro "
Leu Arg Pro Met Thr T r L s " Asp Gly Leu "
Ala Pro Pro Gln His Leu Ile Arg " Leu Leu Gly "
Arg Asn Ser Phe Glu Val Peptides HLA-C GluHisSerAlaTyrGlyG5,558,995 from clone luProArgLysLeuLeuTh MAGE-1 rGlnAs Leu " GluHisSerAlaTyrGlyG"
luProAr LysLeuLeu " SerAlaTyrGlyGluProA"
rgLysLeu GAGE HLA-Cw6 TyrArgProArgProArgA5,648,226 rgTyr " ThrTyrArgProArgProA"
rgArgT r " TyrArgProArgProArgA"
rgTyrV al " ThrTyrArgProArgProA"
r Ar T Val " ArgProArgProArgArgT"
rValGlu " MetSerTrpArgGlyArgS"
erThrTyrArgProArgPro ~g~g " ThrTyrArgProArgProA"
rgArgTyrV alGluProPro GluMetIle MAGE HLA-A1, Isolated nonapeptide5,405,940 primarilyhaving Glu at its N
terminal, Tyr at its C-terminal, and Asp at the third residue from its N terminal, with the proviso that said isolated nonapeptide is not Glu Ala Asp Pro Thr Gly His Ser Tyr (SEQ ID NO:
1 ), and wherein said isolated nonapeptide binds to a human leukocyte antigen molecule on a cell to form a complex, said complex rovokin 1 sis of said cell by a cytolytic T
cell specific to said complex " GluValValProIleSerHis"
LeuT r " GluValValArgIleGlyHi"
sLeuT r " GluValAspProIleGlyHi"
sLeuT
" GluValAspProAlaSerA"
snThrTyr " GluValAspProThrSerA"
snThrT r " GluAlaAspProThrSerA"
snThrTyr " GluValAspProIleGlyHi"
sValTyr " GAAGTGGTCCCCAT "
CAGCCACTTGTAC
" GAAGTGGTCCGCA "
TCGGCCACTTGTAC
" GAAGTGGACCCCA "
TCGGCCACTTGTAC
" GAAGTGGACCCCG "
CCAGCAACACCTAC
" GAAGTGGACCCCA "
CCAGCAACACCTAC
" GAAGCGGACCCCA "
CCAGCAACACCTAC
" GAAGCGGACCCCA "
CCAGCAACACCTAC
" GAAGTGGACCCCA "
TCGGCCACGTGTAC
" GluAlaAspProThrGly"
HisSer " AlaAspProTrpGlyHisS"
erT
MAGE HLA-A2 SerThrLeuValGluValT5,554,724 a tides hrLeuGl GluVa1 " " LeuValGluValThrLeu"
Gl GIuVaI
" " LysMetValGluLeuVa1"
HisPheLeu " " ValIlePheSerLysAlaSe"
rGluT rLeu " " TyrLeuGlnLeuValPhe"
Gl IleGluVa1 " " GInLeuValPheGlyIleG1"
uValVal " " GInLeuValPheGlyIleG1"
uValValGluVal " " IleIleValLeuAlaIleIleA"
laIle " " LysIleTrpGluGluLeuSe"
rMetLeuGluVal " " AlaLeuIleGluThrSerTy"
rValLysVal " " LeuIleGluThrSerTyrVa"
ILysVal " " GlyLeuGluAlaArgGly"
GluAlaLeuG1 Leu " " GlyLeuGIuAlaArgGly"
GIuAlaLeu " " AlaLeuGlyLeuValGly"
AlaGlnAla " " GIyLeuValGlyAlaGln"
AIaProAla " " AspLeuGluSerGluPhe"
GlnAlaAla " " AspLeuGluSerGluPhe"
GlnAlaAlaIle " " AlaIleSerArgLysMetV"
alGluLeuVa1 " " AlaIleSerArgLysMetV"
aIGIuLeu " " LysMetValGluLeuVa1"
HisPheLeuLeu " " LysMetValGluLeuVal"
HisPheLeuLeuLeu " " LeuLeuLeuLysTyrArg"
AlaAr GluProVa1 " " LeuLeuLysTyrArgAla"
Ar GluProVa1 " " ValLeuArgAsnCysGln"
As PhePheProVal " " TyrLeuGInLeuValPhe"
Gl IleGluValVa1 " " GlyIleGluValValGluV"
aIVaIProIle " " ProIleSerHisLeuTyrIle"
LeuVal " " HisLeuTyrIleLeuValTh"
rC sLeu " " HisLeuTyrIleLeuValTh"
rC sLeuGl Leu " " TyrIleLeuValThrCysLe"
uGl Leu " " CysLeuGlyLeuSerTyr"
As Gl Leu " " CysLeuGlyLeuSerTyr"
As G1 LeuLeu " " ValMetProLysThrGIyL"
euLeuIle " " ValMetProLysThrGIyL"
euLeuIlelle " " ValMetProLysThrGlyL"
euLeuIleIleVal " " GlyLeuLeuIleIleValLe"
uAlaIle " " GlyLeuLeuIleIleValLe"
uAlaIleIle " " GlyLeuLeuIleIleValLe"
uAlaIleIleAla " " LeuLeuIleIleValLeuA1"
aIleIle " " LeuLeuIleIleValLeuA1"
aIleIleAla " " LeuLeuIleIleValLeuA1"
aIleIleAlaIle " " - LeuIleIleValLeuAlaIleI"
leAla " " LeuIleIleValLeuAlaIleI"
leAlaIle ' " " IIeIleAlaIleGluGlyAsp"
C sAla " " LysIleTrpGluGluLeuSe"
rMetLeu " " LeuMetGlnAspLeuVa1"
GlnGluAsnT rLeu " " PheLeuTrpGlyProArg"
AlaLeuIle " " LeuIleGluThrSerTyrVa"
1L sVal " " AlaLeuIleGluThrSerTy"
rValL sValLeu " " ThrLeuLysIleGlyGlyG1"
uProHisIle " " HisIleSerTyrProProLeu"
HisGluAr Ala " " GlnThrAlaSerSerSerSe"
rThrLeu " " GlnThrAlaSerSerSerSe"
rThrLeuVal " " ValThrLeuGlyGluValP"
roAlaAla " " ValThrLysAlaGluMetL"
euGluSerVa1 " " ValThrLysAlaGluMetL"
euGluSerValLeu " " VaIThrCysLeuGlyLeu"
SerTyrAs G1 Leu " " LysThrGlyLeuLeuIleI1"
eValLeu " " LysThrGIyLeuLeuIleIl"
eValLeuAla " " LysThrGlyLeuLeuIleI1"
eValLeuAlaIle " " HisThrLeuLysIleGlyGl"
GluProHisIle " " MetLeuAspLeuGlnPro"
GluThrThr Mage-3 HLA-A2 GlyLeuGluAlaArgGly5,585,461 a tides GluAlaLeu " " AlaLeuSerArgLysValA"
IaGluLeu " " PheLeuTrpGlyProArg"
AlaLeuVal " " ThrLeuValGluValThrL"
euGl GluVa1 " " AlaLeuSerArgLysValA"
laGluLeuVal " " AlaLeuValGluThrSerT"
rValL sVal Tyrosinase HLA-A2 TyrMetAsnGlyThrMet5,487,974 SerGlnVal " " MetLeuLeuAlaValLeu"
T sLeuLeu Tyrosinase HLA-A2 MetLeuLeuAlaValLeu5,530,096 T rC sLeu " " LeuLeuAlaValLeuTyr"
C sLeuLeu Tyrosinase HLA-A2 SerGluIleTrpArgAspIle5,519,117 and HLA-B44 As PheAlaHisGluAla " " SerGluIleTrpArgAspIle"
As Phe " " GluGluAsnLeuLeuAsp"
PheValAr Phe Melan EAAGIGIL,TV Jager, E.
et al.
A/MART-1 Granulocyte-macrophage-colony-stimulating Factor Enhances Immune Responses To Melanoma-'associated Peptides in vivo hit. J Cancer 67, 54-62 1996) T rosinase MLLAVLYCL "
" YMDGTMS V "
gp100/Pmel YLEPGPVTA "
" LLDGTATLRL "
Influenza GILGFVFTL "
matrix MAGE-1 EADPTGHSY "
FROM
DAVID'S
LIST
BAGE HLA-C MAARAVFLALSAQL "
LQARLMKE
" " MAARAVFLALSAQL "
LQ
" " AARAVFLAL "
InfluenzaPR8 NP 147-154 Kd IYQRIRALV Falk et al., Allele-specific motifs revealed by sequencing of self peptides eluted from MHC molecules SELF P815 " SYFPEITHI "
PEPTIDE
InfluenzaJap HA " IYATVAGSL "
VYQILAIYA "
" " ~~ IYSTVASSL "
" JAP HA ~~ LYQNVGTYV "
HLA-A24 ~~ RYLENQKRT "
HLA-Cw3 " RYLKNGKET "
P815 " KYQAVTTTL "
PlasmodiumCSP " SYIPSAEKI "
berghen PlasmodiumCSP " SYVPSAFQI "
yoelli VesicularNP 52-59 Kb RGYVYQGL "
stomatitis viruse Ovalbumin " SIINFEKL "
Sandal NP 321-332 " APGNYPAL "
Virus VPYGSFKHV Morel et al., Processing of some antigens by the standard proteasome but not by the immunoproteaso me results in poor presentation by dendritic cells, Immunity, vol.
12:107-117, 2000.
MOTIFS
influenzaPR8 NP Kd restrictedTYQRTRALV 5,747,269 peptide motif self P815 " SYFPEITHI "
a tide influenzaJAP HA " IYATVAGSL "
influenzaJAP HA " VYQILAIYA "
influenzaPR8 HA " IYSTVASSL "
influenzaJAP HA " LYQNVGTYV "
HLA-A24 RYLENGKETL "
HLA-Cw3 RYLKNGKETL "
P815 " KYQAVTTTL "
tumour antigen PlasmodiumCSP " SYIPSAEKI "
ber hei PlasmodiumCSP ~ " SYVPSAEQI "
oeli influenzaNP Db - ASNENMETM "
restricted peptide motif adenovirusElA " SGPSNTPPEI "
lymphocytic " SGVENPGGYCL "
choriomenin gitis simian 40 T " SAINNY . . . "
virus HIV reverse HLA-A2.1-ILKEPVHGV "
transcriptase restricted peptide motif influenza " GILGFVFTL "
matrix rotein influenzainfluenza " ILGFVFTLTV "
matrix rotein HIV Ga rotein FL SRPEPT "
HIV Ga rotein AM MLKE . . "
HIV Ga rotein PIAPG MRE "
HIV Ga rotein MKDCTER "
HLA- VYGVIQK "
A*0205-restricted peptide motif Table S
VSV-NP a tide 49-62 LCMV-NP a tide 118-132 LCMV 1 co rotein a tide. 33-41 ISN LTLDSNTKYFHKLN
ISNQLTLDSNTKYFHKL
ISNQLTLDSNTKYFHK
VDTFLEDVKNLYHSEA
KPRAIVVDPVHGFMY
K TISPDYRNMI
Y DFIMDPKEKDKV
LLSFVRDLN YRADI
LPKPPKPV SKMRMATPL
LPKPPKPV SKMRMATPLLMQALP
LPKPPKPVSKMRMATPLLM ALPM
PKPPKP V SKMRMATPL
PKPPKPVSKMRMATPLLM A
KPPKPVSKMRMATPLLMQ
KPPKPVSKMRMATPLLMQALPM
VDDTQFVRFDSDAAS
ATKYGNMTEDHVMHLLQNA
VFLLLLADKVPETSLS
LNKILLDE A WK
GPPKLDIRKEEK IMIDIFH
GPPKLDIRKEEK IM>DIFHP
GFKAIRPDKKSNPIIRTV
YANILLDRRVP TDMTF
NLFLKSDGRIKYTLNKNSLK
IPDNLFLKSDGRIKYTLNKN
IPDNLFLKSDGRIKYTLNK
IPDNLFLKSDGRIKYTLN
NLFLKSDGRIKYTLNK
NLFLKSDGRIKYTLN
VTTLNSDLKYNALDLTN
VGSDWRFLRGYHQYA
[0078] Still further embodiments are directed to methods, uses, therapies and compositions related to epitopes with specificity for MHC, including, for example, those listed in Tables 6-10. Other embodiments include one or more of the MHCs listed in Tables 6-10, including combinations of the same, while other embodiments specifically exclude any one or more of the MHCs or combinations thereof. Tables 8-10 include frequencies for the listed HLA antigens.
Table 6 Class I MHC Molecules Class I
Human HLA-A*0101 HLA-A*0201 HLA-A*0202 HLA-A*0203 HLA-A*0204 HLA-A*0205 HLA-A*0206 HLA-A*0207 HLA-A*0209 HLA-A*0214 HLA-A*0301 HLA-A* 11 O 1 HLA-A*2902 HLA-A*3101 HLA-A*3302 HLA-A*6801 HLA-A*6901 HLA-B*0702 HLA-B*0703 HLA-B *0704 HLA-B*0705 HLA-B*1501 (B62) HLA-B *2702 HLA-B*2704 HLA-B*2705 HLA-B*2709 HLA-B*3501 HLA-B*3502 HLA-B*3701 HLA-B*3801 HLA-B*39011 HLA-B *3902 HLA-B*40012 (B60) HLA-B*4006 (B61) HLA-B*4402 HLA-B*4403 HLA-B*4501 HLA-B *4601 HLA-B*5101 HLA-B * 5102 HLA-B*5103 HLA-B*5201 HLA-B*5301 HLA-B*5401 HLA-B*5501 HLA-B*5502 HLA-B*5601 HLA-B*5801 HLA-B*6701 HLA-B*7301 HLA-B*7801 HLA-Cw*0102 HLA-Cw*0301 HLA-Cw*0304 HLA-Cw*0401 HLA-Cw *0601 HLA-Cw*0602 HLA-Cw*0702 HLA-Cw8 HLA-Cw*1601 M
HLA-G
Murine H2-Kd H2-Dd H2-Ld H2-Kb H2-Db H2-K'' H2-K'""' Qa-la Qa-2 Rat RT 1.Aa RT 1.A' Bovine Bota-Al l Bota-A20 Chicken Chimpanzee Patr-A*04 Patr-A* 11 Patr-B*01 Patr-B * 13 Patr-B * 16 Baboon Papa-A*06 Macaque Mamu-A*01 Swine SLA (haplotype d/d) Virus homolog hCMV class I homolog UL18 Table 7 Class I MHC Molecules Class I
Human HLA-Al HLA-A*0101 HLA-A*0201 HLA-A*0202 HLA-A*0204 HLA-A*0205 HLA-A*0206 HLA-A*0207 HLA-A*0214 HLA-A* 11 O 1 HLA-A*2902 HLA-A*3101 HLA-A*3302 HLA-A*6801 HLA-A*6901 HLA-B*0702 HLA-B *0703 HLA-B*0704 HLA-B *0705 HLA-B*1501 (B62) HLA-B *2702 HLA-B *2705 HLA-B*3501 HLA-B*3502 HLA-B*3701 HLA-B*3801 HLA-B*39011 HLA-B*3902 HLA-B*40012 (B60) HLA-B*4006 (B61) HLA-B*4402 HLA-B*4403 HLA-B *4641 HLA-B*5101 HLA-B*5102 HLA-B*5103 HLA-B*5201 HLA-B*5301 HLA-B * 5401 HLA-B*5501 HLA-B*5502 HLA-B*5601 HLA-B*5801 HLA-B *6701 HLA-B*7301 HLA-B*7801 HLA-Cw*0102 HLA-Cw*0301 HLA-Cw*0304 HLA-Cw*0401 HLA-Cw*0601 HLA-Cw*0602 HLA-Cw*0702 HLA-G
Murine H2-K'' H2-Dd H2-Ld H2-Kb H2-Db H2-Kk H2-K'""' Qa-2 Rat RTl .A~
RT1.A~
Bovine Bota-Al l Bota-A20 Chicken Virus homolog hCMV class I homolog UL18 Table 8 [0079) Estimated gene frequencies of HLA-A antigens CAU AFR ASI LAT NAT
Antigen G~ SEb Gf SE Gf SE Gf SE Gf SE
A1 15.18430.04895.72560.07714.48180.08467.40070.097812.03160.2533 A2 28.65350.061918.88490.131724.63520.179428.11980.170029.34080.3585 A3 13.38900.04638.44060.09252.64540.06558.07890.101911.02930.2437 A28 4.46520.02809.92690.09971.76570.05378.94460.10675.38560.1750 A36 0.02210.00201.88360.04480.01480.00490.15840.01480.15450.0303 A23 1.82870.018110.20860.10100.32560.02312.92690.06281.99030.1080 A24 9.32510.03952.96680.056022.03910.172213.26100.127112.66130.2590 A9 unsplit0.08090.00380.03670.00630.08580.01190.05370.00860.03560.0145 A9 total11.23470.042913.21210.112822.45050.173316.24160.138214.68720.2756 A25 2.11570.01950.43290.02160.09900.01281.19370.04041.45200.0924 A26 3.87950.02622.82840.05474.66280.08623.26120.06622.42920.1191 A34 0.15080.00523.52280.06101.35290.04700.49280.02600.31500.0432 A43 0.00180.00060.03340.00600.02310.00620.00550.00280.00590.0059 A66 0.01730.00180.22330.01550.04780.00890.03990.00740.05340.0178 A10 unsplit0.07900.00380.09390.01010.12550.01440.06470.00940.02980.0133 A10 total6.24410.03287.13480.08506.31110.09935.05780.08164.28530.1565 A29 3.57960.02523.20710.05821.12330.04294.51560.07743.43450.1410 A30 2.50670.021213.09690.11292.20250.05984.48730.07722.53140.1215 A31 2.73860.02211.65560.04203.60050.07614.83280.08006.08810.1855 A32 3.69560.02561.53840.04051.03310.04112.70640.06042.55210.1220 A33 1.20800.01486.56070.08229.27010.11912.65930.05991.07540.0796 A74 0.02770.00221.99490.04610.05610.00960.20270.01670.10680.0252 A19 unsplit0.05670.00320.20570.01490.09900.01280.12110.01290.04750.0168 A19 total13.81290.046828.25930.150417.38460.155519.52520.148115.83580.2832 AX 0.82040.02974.95060.09632.99160.11771.63320.08781.84540.1925 Gene frequency.
bStandard error.
Table 9 Estimated gene frequencies for HLA-B antigens CAU AFR ASI LAT NAT
AntigenG~ SE Gf SE Gf SE Gf SE Gf SE
B7 12.17820.044510.59600.10244.26910.08276.44770.091810.98450.2432 B8 9.40770.03973.83150.06341.33220.04673.82250.07158.57890.2176 B 13 2.30610.02030.81030.02954.92220.08861.26990.04161.74950.1013 B 14 4.34810.02773.03310.05660.50040.02875.41660.08462.98230.1316 B 18 4.79800.02903.20570.05821.12460.04294.23490.07523.34220.1391 B27 4.38310.02781.29180.03722.23550.06032.37240.05675.19700.1721 B35 9.66140.04028.51720.09278.12030.112214.65160.132910.11980.2345 B37 1.40320.01590.59160.02521.23270.04490.78070.03270.97550.0759 B41 0.92110.01290.81830.02960.13030.01471.28180.04180.47660.0531 B42 0.06080.00335.69910.07680.08410.01180.58660.02840.28560.0411 B46 0.00990.00130.01510.00404.92920.08860.02340.00570.02380.0119 B47 0.20690.00610.13050.01190.09560.01260.18320.01590.21390.0356 B48 0.08650.00400.13160.01192.02760.05751.59150.04661.02670.0778 B53 0.46200.009210.95290.10390.43150.02661.69820.04811.08040.0798 CAU AFR ASI LAT NAT
AntigenGf SE Gf SE Gf SE Gf SE Gf SE
B59 0.00200.00060.00320.00190.42770.02650.00550.00280' B67 0.00400.00090.00860.00300.22760.01940.00550.00280.00590.0059 B70 0.32700.00777.35710.08660.89010.03821.92660.05120.69010.0639 B73 0.01080.00140.00320.00190.01320.00470.02610.00600' B51 5.42150.03072.59800.05257.47510.10806.81470.09436.90770.1968 B52 0.96580.01321.37120.03833.51210.07522.24470.05520.69600.0641 B5 unsplit0.15650.00530.15220.01280.12880.01460.15460.01460.13070.0278 B5 total6.54380.04354.12140.074711.11600.15049.21410.13247.73440.2784 B44 13.48380.04657.01370.08475.68070.09489.92530.112111.80240.2511 B45 0.57710.01024.80690.07080.18160.01731.88120.05060.76030.0670 B12 0.07880.00380.02800.00550.00490.00290.01930.00510.06540.0197 unsplit B12 14.14400.047411.84860.10725.86730.096311.82580.121012.62810.2584 total 6.9421 B62 5.91170.03201.52670.04049.22490.11904.18250.0747 p,1973 0.3738 B63 0.43020.00881.88650.04480.44380.02700.80830.0333 p,p471 0.0356 B75 0.01040.00140.02260.00491.96730.05660.11010.0123 0.0145 p B76 0.00260.00070.00650.00260.08740.01200.00550.0028 B77 0.00570.00100.01190.00360.05770.00980.00830.0034 0.0059 0.0059 B 15 0.13050.00490.06910.00860.43010.02660.18200.0158 p,p206 unsplit 0.0715 B15 6.49100.03343.52320.060812.21120.13445.29670.0835 p,2035 total 7.4290 B38 2.44130.02090.33230.01893.28180.07281.96520.05171.10170.0806 B39 1.96140.01881.28930.03712.03520.05766.30400.09094.55270.1615 B16 0.06380.00340.02370.00510.06440.01030.12260.01300.05930.0188 unsplit B16 4.46670.02801.64530.04195.38140.09218.39170.10365.71370.1797 total B57 3.59550.02525.67460.07662.57820.06472.18000.05442.72650.1260 B58 0.71520.01145.95460.07844.01890.08031.24810.04130.93980.0745 B 17 0.28450.00720.32480.01870.37510.02480.14460.01410.26740.0398 unsplit B17 4.59520.028411.95400.10766.97220.10413.57270.06913.93380.1503 total B49 1.64520.01722.62860.05280.24400.02002.33530.05621.54620.0953 B50 1.05800.01380.86360.03040.44210.02701.88830.05070.78620.0681 B21 0.07020.00360.02700.00540.01320.00470.07710.01030.03560.0145 unsplit B21 2.77330.02223.51920.06080.69930.03394.30070.07552.36800.1174 total B54 0.01240.00150.01830.00442.68730.06600.02890.00630.05340.0178 B55 1.90460.01850.48950.02292.24440.06040.95150.03611.40540.0909 B56 0.55270.01000.26860.01700.82600.03680.35960.02220.33870.0448 B22 0.16820.00550.04960.00730.27300.02120.03720.00710.12460.0272 unsplit B22 2.08520.02170.82610.02976.03070.09711.37710.04331.92210.1060 total B60 5.22220.03021.52990.04048.32540.11352.25380.05535.72180.1801 B61 1.19160.01470.47090.02256.20720.09894.66910.07882.60230.1231 B40 0.26960.00700.03880.00650.32050.02300.24730.01840.22710.0367 unsplit B40 6.68340.03382.03960.046514.85310.14627.17020.09638.55120.2168 total BX 1.09220.02523.52580.08023.87490.09882.52660.0807( 1.98670.1634 ~
Gene frequency. bStandard error. °The observed gene count was zero.
Table 10.
Estimated gene frequencies of HLA-DR antigens CAU AFR ASI LAT NAT
Antigen G~ SEb Gf Gf SE Gf SE Gf SE
SE
DR1 10.22790.04136.82000.08323.46280.07477.98590.10138.25120.2139 DR2 15.24080.049116.23730.122218.61620.160811.23890.118215.39320.2818 DR3 10.87080.042413.30800.11244.72230.08677.89980.100810.25490.2361 DR4 16.75890.05115.70840.076515.46230.149020.53730.152019.82640.3123 DR6 14.39370.047918.61170.129113.44710.140417.02650.141114.80210.2772 DR7 13.28070.046310.13170.09976.92700.104010.67260.11 10.42190.2378 DR8 2.88200.02276.26730.08006.54130.10139.77310.11106.00590.1844 DR9 1.06160.01392.96460.05599.75270.12181.07120.03832.86620.1291 DR10 1.47900.01632.03970.04652.23040.06021.80440.04951.08960.0801 DR11 9.31800.039610.61510.10184.73750.08697.04110.09555.31520.1740 DR12 1.90700.01854.11520.065510.13650.12391.72440.04842.01320.1086 DR5 unsplit1.21990.01492.29570.04931.41180.04801.82250.04981.67690.0992 DR5 total12.44490.004517.02600.124316.28580.151610.58800.11489.00520.2218 DRX 1.35980.03420.88530.07602.55210.10891.40230.09302.08340.2037 ''Gene frequency.
bStandard error.
[0080] It can be desirable to express housekeeping peptides in the context of a larger protein. Processing can be detected even when a small number of amino acids are present beyond the terminus of an epitope. Small peptide hormones are usually proteolytically processed from longer translation products, often in the size range of approximately 60-120 amino acids. This fact has led some to assume that this is the minimum size that can be efficiently translated. In some embodiments, the housekeeping peptide can be embedded in a translation product of at least about 60 amino acids, in others 70, 80, 90 amino acids, and in still others 100, 110 or 120 amino acids, for example. In other embodiments the housekeeping peptide can be embedded in a translation product of at least about 50, 30, or 15 amino acids.
[0081] Due to differential proteasomal processing, the immunoproteasome of the pAPC
produces peptides that are different from those produced by the housekeeping proteasome in peripheral body cells. Thus, in expressing a housekeeping peptide in the context of a larger protein, it is preferably expressed in the pAPC in a context other than its full-length native sequence, because, as a housekeeping epitope, it is generally only efficiently processed from the native protein by the housekeeping proteasome, which is not active in the pAPC. In order to encode the housekeeping epitope in a DNA sequence encoding a larger polypeptide, it is useful to find flanking areas on either side of the sequence encoding the epitope that permit appropriate cleavage by the immunoproteasome in order to liberate that housekeeping epitope. Such a sequence promoting appropriate processing is referred to hereinafter as having substrate or liberation sequence function.
Altering flanking amino acid residues at the N-terminus and C-terminus of the desired housekeeping epitope can facilitate appropriate cleavage and generation of the housekeeping epitope in the pAPC.
Sequences embedding housekeeping epitopes can be designed de novo and screened to determine which can be successfully processed by immunoproteasomes to liberate housekeeping epitopes.
[0082] Alternatively, another strategy is very effective for identifying sequences allowing production of housekeeping epitopes in APC. A contiguous sequence of amino acids can be generated from head to tail arrangement of one or more housekeeping epitopes.
A construct expressing this sequence is used to immunize an animal, and the resulting T
cell response is evaluated to determine its specificity to one or more of the epitopes in the array. These immune responses indicate housekeeping epitopes that are processed in the pAPC
effectively. The necessary flanking areas around this epitope are thereby defined. The use of flanking regions of about 4-6 amino acids on either side of the desired peptide can provide the necessary information to facilitate proteasome processing of the housekeeping epitope by the immunoproteasome.
Therefore, a substrate or liberation sequence of approximately 16-22 amino acids can be inserted into, or fused to, any protein sequence effectively to result in that housekeeping epitope being produced in an APC. In some embodiments, a broader context of a substrate sequence can also influence processing. In such embodiments, comparisons of a liberaton sequence in a variety of contexts can be useful in further optimizing a particular substrate sequence. In alternate embodiments the whole head-to-tail array of epitopes, or just the epitopes immediately adjacent to the correctly processed housekeeping epitope can be similarly transferred from a test construct to a vaccine vector.
[0083] In a preferred embodiment, the housekeeping epitopes can be embedded between known immune epitopes, or segments of such, thereby providing an appropriate context for processing. The abutment of housekeeping and immune epitopes can generate the necessary context to enable the immunoproteasome to liberate the housekeeping epitope, or a larger fragment, preferably including a correct C-terminus. It can be useful to screen constructs to verify that the desired epitope is produced. The abutment of housekeeping epitopes can generate a site cleavable by the immunoproteasome. Some embodiments of the invention employ known epitopes to flank housekeeping epitopes in test substrates; in others, screening as described below is used, whether the flanking regions are arbitrary sequences or mutants of the natural flanking sequence, and whether or not knowledge of proteasomal cleavage preferences are used in designing the substrates.
[0084] Cleavage at the mature N-terminus of the epitope, while advantageous, is not required, since a variety of N-terminal trimming activities exist in the cell that can generate the mature N-terminus of the epitope subsequent to proteasomal processing. It is preferred that such N-terminal extension be less than about 25 amino acids in length and it is further preferred that the extension have few or no proline residues. Preferably, in screening, consideration is given not only to cleavage at the ends of the epitope (or at least at its C-terminus), but consideration also can be given to ensure limited cleavage within the epitope.
[0085] Shotgun approaches can be used in designing test substrates and can increase the efficiency of screening. In one embodiment multiple epitopes can be assembled one after the other, with individual epitopes possibly appearing more than once. The substrate can be screened to determine which epitopes can be produced. In the case where a particular epitope is of concern, a substrate can be designed in which it appears in multiple different contexts.
When a single epitope appearing in more than one context is liberated from the substrate additional secondary test substrates, in which individual instances of the epitope are removed, disabled, or are unique, can be used to determine which are being liberated and truly confer substrate or liberation sequence function.
[0086] Several readily practicable screens exist. A preferred in vitro screen utilizes proteasomal digestion analysis, using purified immunoproteasomes, to determine if the desired housekeeping epitope can be liberated from a synthetic peptide embodying the sequence in question.
The position of the cleavages obtained can be determined by techniques such as mass spectrometry, HPLC, and N-terminal pool sequencing; as described in greater detail in U.S.
Patent Application Nos. 09/561,074, 09/560,465 and 10/117,937, and Provisional U.S. Patent Application Nos.
60/282,211, 60/337,017, and 60/363, 210.
[0087] Alternatively, in vivo and cell-based screens such as immunization or target sensitization can be employed. For immunization a nucleic acid construct capable of expressing the sequence in question is used. Harvested CTL can be tested for their ability to recognize target cells presenting the housekeeping epitope in question. Such targets cells are most readily obtained by pulsing cells expressing the appropriate MHC molecule with synthetic peptide embodying the mature housekeeping epitope. Alternatively, immunization can be carried out using cells known to express housekeeping proteasome and the antigen from which the housekeeping epitope is derived, either endogenously or through genetic engineering. To use target sensitization as a screen, CTL, or preferably a CTL clone, that recognizes the housekeeping epitope can be used.
In this case it is the target cell that expresses the embedded housekeeping epitope (instead of the pAPC during immunization) and it must express immunoproteasome. Generally, the cell or target cell can be transformed with an appropriate nucleic acid construct to confer expression of the embedded housekeeping epitope. Loading with a synthetic peptide embodying the embedded epitope using peptide loaded liposomes, or complexed with cationic lipid protein transfer reagents such as BIOPORTERTM (Gene Therapy Systems, San Diego, CA), represents an alternative.
[0088] Once sequences with substrate or liberation sequence function are identified they can be encoded in nucleic acid vectors, chemically synthesized, or produced recombinantly. In any of these forms they can be incorporated into immunogenic compositions. Such compositions can be used in vitro in vaccine development or in the generation or expansion of CTL
to be used in adoptive immunotherapy. In vivo they can be used to induce, amplify or sustain and active immune response.
The uptake of polypeptides for processing and presentation can be greatly enhanced by packaging with cationic lipid, the addition of a tract of cationic amino acids such as poly-L-lysine (Ryser, H.J.
et al., J. Cell Physiol. 113:167-178, 1982; Shen, W.C. & Ryser, H.J., Proc.
Natl. Aced. Sci. USA
75:1872-1876, 1978), the incorporation into branched structures with importation signals (Sheldon, K. et al., Proc. Natl. Aced. Sci. USA 92:2056-2060, 1995), or mixture with or fusion to polypeptides with protein transfer function including peptide earners such as pep-1 (Morris, M.C., et al., Nat.
Biotech. 19:1173-1176, 2001), the PreS2 translocation motif of hepatitis B
virus surface antigen, VP22 of herpes viruses, and HIV-TAT protein (Oess, S. & Hildt, E., Gene Ther.
7:750-758, 2000;
Ford, K.G., et al., Gene Ther. 8:1-4, 2001; Hung, C.F. et al., J. virol.
76:2676-2682, 2002; Oliveira, S.C., et a;. Hum. Gene Ther. 12:1353-1359, 2001; Normand, N. et al., J. Biol.
Chem. 276:15042-15050, 2001; Schwartz, J.J. & Zhang, S., Curr. Opin. Mol. Ther. 2:162-167, 2000; Elliot G., 7 Hare, P. Cell 88:223-233, 1997), among other methodologies. Particularly for fusion proteins the immunogen can be produced in culture and the purified protein administered or, in the alternative, the nucleic acid vector can be administered so that the immunogen is produced and secreted by cells transformed in vivo. In either scenario the transport function of the fusion protein facilitates uptake by pAPC.
EXAMPLES
Example 1 [0089] A recombinant DNA plasmid vaccine, pMA2M, which encodes one polypeptide with an HLA A2-specific CTL epitope ELAGIGIL,TV (SEQ ID NO. 1) from melan-A
(26-35A27L), and a portion (amino acids 31-96) of melan-A (SEQ ID NO. 2) including the epitope clusters at amino acids 31-48 and 56-69, was constructed. These clusters were previously disclosed in U.S.
Patent Application No. 09/561,571 entitled EPITOPE CLUSTERS. Flanking the defined melan-A
CTL epitope are short amino acid sequences derived from human tyrosinase (SEQ
ID NO. 3) to facilitate liberation of the melan-A housekeeping epitope by processing by the immunoproteasome.
In addition, these amino acid sequences represent potential CTL epitopes themselves. The cDNA
sequence for the polypeptide in the plasmid is under the control of promoter/enhancer sequence from cytomegalovirus (CMVp) (see Figure 1), which allows efficient transcription of messenger for the polypeptide upon uptake by APCs. The bovine growth hormone polyadenylation signal (BGH
polyA) at the 3' end of the encoding sequence provides a signal for polyadenylation of the messenger to increase its stability as well as for translocation out of nucleus into the cytoplasm for translation.
To facilitate plasmid transport into the nucleus after uptake, a nuclear import sequence (I~IIS) from simian virus 40 (SV40) has been inserted in the plasmid backbone. The plasmid carries two copies of a CpG immunostimulatory motif, one in the NIS sequence and one in the plasmid backbone.
Lastly, two prokaryotic genetic elements in the plasmid are responsible for amplification in E.coli, the kanamycin resistance gene (Kan R) and the pMB 1 bacterial origin of replication.
SUBSTRATE or LIBERATION sequence [0090] The amino acid sequence of the encoded polypeptide (94 amino acid residues in length) (SEQ ID NO. 4) containing a 28 amino acid substrate or liberation sequence at its N-terminus (SEQ ID NO. 5) is given below:
[0091] MLLAVLYCL-ELAGIGILTV-YMDGTMSQV-GILTVILGVLLLIGCWYCRRRNGYRALMDKSLHVGTQCALTRRCPQEGFDHRDSKVSLQEK
NCEPV
[0092] The first 9 amino acid residues are derived from tyrosinase~_9 (SEQ ID
NO. 6), the next ten constitute melan-A (26-35A27L) (SEQ )D NO. 1), and amino acid residues 20 to 29 are derived from tyrosinase369-377 (SEQ >D NO. 7). These two tyrosinase nonamer sequences both represent potential HLA A2-specific CTL epitopes. Amino acid residues 10-19 constitute melan-A
(26-35A27L) an analog of an HLA A2-specific CTL epitope from melan-A, EAAGIGILTV (SEQ ID
NO. 8), with an elevated potency in inducing CTL responses during in vitro immunization of human PBMC and in vivo immunization in mice. The segment of melan-A constituting the rest of the polypeptide (amino acid residues 30 to 94) contain a number of predicted HLA
A2-specific epitopes, including the epitope clusters cited above, and thus can be useful in generating a response to immune epitopes as described at length in the patent applications 'Epitope Synchronization in Antigen Presenting Cells' and 'Epitope Clusters'. This region was also included to overcome any difficulties that can be associated with the expression of shorter sequences. A drawing of pMA2M is shown in Figure 1.
Plasmid construction [0093] A pair of long complementary oligonucleotides was synthesized which encoded the first 30 amino acid residues. In addition, upon annealing, these oligonucleotides generated the cohensive ends of Afl II at the 5' end and that of EcoR I at the 3' end. The melan A3,_96 region was amplified with PCR using oligonucleotides carrying restriction sites for EcoR
I at the 5' end and Not I at the 3' end. The PCR product was digested with EcoR I and Not I and ligated into the vector backbone, described in Example 1, that had been digested with Afl II and Not I, along with the annealed oligonucleotides encoding the amino terminal region in a three-fragment ligation. The entire coding sequence was verified by DNA sequencing. The sequence of the entire insert, from the Afl II site at the 5' end to the Not I site at the 3' end is disclosed as SEQ
ID NO. 9. Nucleotides 12-293 encode the polypeptide.
Example 2 [0094] Three vectors containing melan-A (26-35A27L) (SEQ B7 NO. 1) as an embedded housekeeping epitope were tested for their ability to induce a CTL
response to this epitope in HLA-A2 transgenic HHD mice (Pascolo et al. J. Exp. Med. 185:2043-2051, 1997). One of the vectors was pMA2M described above (called pVAXM3 in Figure 3). In pVAXM2 the same basic group of 3 epitopes was repeated several times with the flanking epitopes truncated by differing degrees in the various repeats of the array. Specifically the cassette consisted o~
[0095] M-Tyr(5-9)-ELA-Tyr(369-373)-Tyr(4-9)-ELA-Tyr(369-374)-Tyr(3-9)-ELA-Tyr(369-375)-Tyr(2-9)-ELA
(SEQ ID NO. 10) [0096] where ELA represents melan-A (26-35A27L) (SEQ >D NO. 1). This cassette was inserted in the same plasmid backbone as used for pVAXM3. The third, pVAXMI is identical to pVAXM2 except that the epitope array is followed by an IRES (internal ribosome entry site for encephalomyocarditis virus) linked to a reading frame encoding melan-A 31-70.
[0097] Four groups of three HHD A2.1 mice were injected intranodally in surgically exposed inguinal lymph nodes with 25 pl of 1 mg/ml plasmid DNA in PBS on days 0, 3, and 6, each group receiving one of the three vectors or PBS alone. On day 14 the spleens were harvested and restimulated in vitro one time with 3-day LPS blasts pulsed with peptide (melan-A (26-35A27L)(SEQ ID NO. 1)). The in vitro cultures were supplemented with Rat T-Stim (Collaborative Biomedical Products) on the 3'd day and assayed for cytolytic activity on the 7'" day using a standard 51 Cr-release assay. Figures 2 to 5 show % specific lysis obtained using the cells immunized with PBS, pVAXMl, pVAXM2, and pVAXM3, respectively on T2 target cells and T2 target cells pulsed with melan-A (26-35A27L) (ELA) (SEQ ID NO. 1). All three vectors generated strong CTL
responses. These data indicated that the plasmids have been taken up by APCs, the encoded polypeptide has been synthesized and proteolytically processed to produce the decamer epitope in question (that is, it had substrate or liberation sequence function), and that the epitope became HLA-A2 bound for presentation. Also, an isolated variant of pVAXM2, that terminates after the 55'"
amino acid, worked similarly well as the full length version (data not shown).
Whether other potential epitopes within the expression cassette can also be produced and be active in inducing CTL
responses can be determined by testing for CTL activity against target cells pulsed with corresponding synthetic peptides.
Example 3 An NY-ESO-1 (SEQ ID NO. 11 ) SUBSTRATE/LIBERATION Sequence [0098] Six other epitope arrays were tested leading to the identification of a substrate/liberation sequence for the housekeeping epitope NY-ESO-1,57_165 (SEQ 117 NO. 12). The component epitopes of the arrays were:
[0099]SSX-24~-49: KASEKIFYV (SEQ ID NO. Array element 13) A
[O100JNY-ESO-1157-165SLLMWITQC (SEQ ID NO. Array element 12) B
[0101]NY-ESO-1 ~ TQCFLPVFL (SEQ m NO. Array element 63_ ~ ~ ~ 14) C
:
[0102]PSMA2gg_297: GLPS1PVHPI(SEQ ID NO. Array element 15) D
[0103]TYR4_9: AVLYCL (SEQ ID NO. Array element 16) E
[0104]The six arraysthe following had arrangements of elements after starting with an initiator methionine:
[OlOSJpVAX-PC-A: B-A-D-D-A-B-A-A
[0106]pVAX-PC-B: D-A-B-A-A-D-B-A
[0107)pVAX-PC-C: E-A-D-B-A-B-E-A-A
[0108]pVAX-BC-A: B-A-C-B-A-A-C-A
[0109)pVAX-BC-B: C-A-B-C-A-A-B-A
[0110] pVAX-BC-C: E-A-A-B-C-B-A-A
[0111] These arrays were inserted into the same vector backbone described in the examples above. The plasmid vectors were used to immunize mice essentially as described in Example 2 and the resulting CTL were tested for their ability to specifically lyse target cells pulsed with the peptide NY-ESO-1 157-165, corresponding to element B above. Both pVAX-PC-A and pVAX-BC-A were found to induce specific lytic activity. Comparing the contexts of the epitope (element B) in the various arrays, and particularly between pVAX-PC-A and pVAX-BC-A, between pVAX-PC-A and pVAX-PC-B, and between pVAX-BC-A and pVAX-BC-C, it was concluded that it was the first occurrence of the epitope in pVAX-PC-A and pVAX-BC-A that was being correctly processed and presented. In other words an initiator methionine followed by elements B-A constitute a substrate/liberation sequence for the presentation of element B. On this basis a new expression cassette for use as a vaccine was constructed encoding the following elements:
[0112] An initiator methionine, [0113] NY-ESO-1 ~ 57-165 (bold) - a housekeeping epitope, [0114] SSX24~-49 (italic) -providing appropriate context for processing, and [0115] NY-ESO-1 ~~_ ~ gp - to avoid "short sequence" problems and provide immune epitopes.
[0116) Thus the construct encodes the amino acid sequence:
[0117] M-SLLMWITQC-KASEKIFYV
RCGARGPESRLLEFYLAMPFATPMEAELARRSLAQDAPPLPVPGVLLKEFTVSGNIL,TIRLTA
ADHRQLQLSISSCLQQLSLLMWITQCFLPVFLAQPPSGQRR (SEQ ID NO. 17) and MSLLMWITQCKASEKIFYV (SEQ ID NO. 18) constitutes the liberation or substrate sequence. A
polynucleotide encoding SEQ ID NO. 17 (SEQ ID NO. 19: nucleotides 12-380) was inserted into the same plasmid backbone as used for pMA2M generating the plasmid pN157.
Example 4 [0118] A construct similar to pN157 containing the whole epitope array from pVAX-PC-A was also made and designated pBPL. Thus the encoded amino acid sequence in pBPL is:
[0119] M-SLLMWITQC-KASEKIFYY GLPSIPVHPI-GLPSIPVHPI-KASEKIFYV
SLLMWITQC-KASEKIFYV KASEKIFYV
RCGARGPESRLLEFYLAMPFATPMEAELARRSLAQDAPPLPVPGVLLKEFTVSGNIL,TIRLTA
ADHRQLQLSISSCLQQLSLLMWITQCFLPVFLAQPPSGQRR (SEQ m NO. 20).
[0120] SEQ LD NO. 21 is the polynucleotide encoding SEQ ID NO. 20 used in pBPL.
[0121] A portion of SEQ ID NO. 20, IKASEKIFYVSLLMWITQCKASEKIFYVK (SEQ
m NO. 22) was made as a synthetic peptide and subjected to in vitro proteasomal digestion analysis with human immunoproteasome, utilizing both mass spectrometry and N-terminal pool sequencing.
The identification of a cleavage after the C residue indicates that this segment of the construct can function as a substrate or liberation sequence for NY-ESO-1 ~5~_~65 (SEQ ID
NO. 12) epitope (see Figure 6). Figure 7 shows the differential processing of the SLLMWITQC epitope (SEQ ID NO. 12) in its native context where the cleavage following the C is more efficiently produced by housekeeping than immunoproteasome. The immunoproteasome also produces a major cleavage internal to the epitope, between the T and the Q when the epitope is in its native context, but not in the context of SEQ ID NO. 22 (compare fig. 6 and 7).
Example 5 [0122] Screening of further epitope arrays led to the identification of constructs promoting the expression of the epitope SSX-24_49 (SEQ ID NO. 13). In addition to some of the array elements defined in Example 3, the following additional elements were also used:
[0123) SSX-457-65:VMTKLGFKV (SEQ lD NO. 23) Array element F.
[0124] PSMA730-739 RQ~~TV (SEQ ID NO. 24) Array element G.
[0125] A construct, denoted CTLA02, encoding an initiator methionine and the.
array F-A-G-D-C-F-G-A, was found to successfully immunize HLA-A2 transgenic mice to generate a CTL
response recognizing the peptide SSX-241-49 (SEQ 117 NO. 13).
[0126] As described above, it can be desirable to combine a sequence with substrate or liberation sequence function with one that can be processed into immune epitopes. Thus SSX-2 ~ 5_ 183 (SEQ ~ NO. 25) was combined with all or part of the array as follows:
[0127] CTLS 1: F-A-G-D-C-F-G-A- SSX-2 ~ 5_ ~ g3 (SEQ 1D NO. 26) [0128] CTLS2: SSX-2 ~ 5_ ~ 83 - F-A-G-D-C-F-G-A (SEQ ID NO. 27) [0129] CTLS3: F-A-G-D- SSX-215-~ 83 (SEQ ID NO. 28) [0130] CTLS4: SSX-2~5_~g3 -C-F-G-A (SEQ ID NO. 29).
[0131] All of the constructs except CTLS3 were able to induce CTL recognizing the peptide SSX-24_49 (SEQ >D NO. 13). CTLS3 was the only one of these four constructs which did not include the second element A from CTLA02 suggesting that it was this second occurrence of the element that provided substrate or liberation sequence function. In CTLS2 and CTLS4.the A element is at the C-terminal end of the array, as in CTLA02. In CTLS1 the A element is immediately followed by the SSX-2 ~ 5_ ~ g3 segment which begins with an alanine, a residue often found after proteasomal cleavage sites (Toes, R.E.M., et al., J. Exp. Med. 194:1-12, 2001). SEQ )D NO. 30 is the polynucleotide sequence encoding SEQ ID NO. 26 used in CTLS I, also called pCBP.
(0132] A portion of CTLS1 (SEQ ID NO. 26), encompassing array elements F-A-SSX-215-23 with the sequence RQIYVAAFTV-KASEKIFYY AQIPEKIQK (SEQ ID NO. 31 ), was made as a synthetic peptide and subjected to in vitro proteasomal digestion analysis with human immunoproteasome, utilizing both mass spectrometry and N-terminal pool sequencing. The observation that the C-terminus of the SSX-241-49 epitope (SEQ ID NO. 13) was generated (see Figure 8) provided further evidence in support of substrate or liberation sequence function. The data in Figure 9 showed the differential processing of the SSX-24~-49 epitope, KASEKIFYh (SEQ >D NO.
13), in its native context, where the cleavage following the V was the predominant cleavage produced by housekeeping proteasome, while the immunoproteasome had several major cleavage sites elsewhere in the sequence. By moving this epitope into the context provided by SEQ >D NO. 31 the desired cleavage became a major one and its relative frequency compared to other immunoproteasome cleavages was increased (compare figs. 8 and 9). The data in figure 8B also showed the similarity in specificity of mouse and human immunoproteasome lending support to the usefulness of the transgenic mouse model to predict human antigen processing.
Example 6 [0133] Screening also revealed substrate or liberation sequence function for a tyrosinase epitope, Tyr2o~-215 (SEQ >D NO. 32), as part of an array consisting of the sequence [Tyre _ ~ 7- Tyr2o7-215]4~ ~MLLAVLYCLLWSFQTSA-FLPWHRLFL]4, (SEQ ID NO. 33). The same vector backbone described above was used to express this array. This array differs from those of the other examples in that the Tyr~_~7 segment, which was included as a source of immune epitopes, is used as a repeated element of the array. This is in contrast with the pattern shown in the other examples where sequence included as a source of immune epitopes and/or length occurred a single time at the beginning or end of the array, the remainder of which was made up of individual epitopes or shorter sequences.
Plasmid construction [0134] The polynucleotide encoding SEQ ID NO. 33 was generated by assembly of annealed synthetic oligonucleotides. Four pairs of complementary oligonucleotides were synthesized which span the entire coding sequence with cohesive ends of the restriction sites of Afl II and EcoR I
at either terminus. Each complementary pair of oligonucleotides were first annealed, the resultant DNA fragments were ligated stepwise, and the assembled DNA fragment was inserted into the same vector backbone described above pre-digested with Afl II/EcoR I. The construct was called CTLT2/pMEL and SEQ 117 NO. 34 is the polynucleotide sequence used to encode SEQ 117 NO. 33.
Example 7 Administration of a DNA ~lasmid formulation of a immunotherapeutic for melanoma to humans.
[0135] An MA2M melanoma vaccine with a sequence as described in Example 1 above, was formulated in 1 % Benzyl alcohol, I % ethyl alcohol, O.SmM EDTA, citrate-phosphate, pH 7.6.
Aliquots of 200, 400, and 600 pg DNA/ml were prepared for loading into MIhIIMED 407C infusion pumps. The catheter of a SILHOUETTE infusion set was placed into an inguinal lymph node visualized by ultrasound imaging. The pump and infusion set assembly was originally designed for the delivery of insulin to diabetics. The usual l7mm catheter was substituted with a 3lmm catheter for this application. The infizsion set was kept patent for 4 days (approximately 96 hours) with an infusion rate of about 25 pl/hour resulting in a total infused volume of approximately 2.4 ml. Thus the total administered dose per infusion was approximately 500, and 1000 pg;
and can be 1500 pg, respectively, for the three concentrations described above. Following an infusion, subjects were given a 10 day rest period before starting a subsequent infusion. Given the continued residency of plasmid DNA in the lymph node after administration and the usual kinetics of CTL response following disappearance of antigen, this schedule will be sufficient to maintain the immunologic CTL response.
Example 8 [0136] SEQ 1D NO. 22 is made as a synthetic peptide and packaged with a cationic lipid protein transfer reagent. The composition is infused directly into the inguinal lymph node (see example 7) at a rate of 200 to 600 pg of peptide per day for seven days, followed by seven days rest.
An initial treatment of 3-8 cycles are conducted.
Example 9 [0137) A fusion protein is made by adding SEQ )D NO. 34 to the 3' end of a nucleotide sequence encoding herpes simplex virus 1 VP22 (SEQ )D NO. 42) in an appropriate mammalian expression vector; the vector used above is suitable. The vector is used to transform HEK 293 cells and 48 to 72 hours later the cells are pelleted, lysed and a soluble extract prepared. The fusion protein is purified by affinity chromatagraphy using an anti-VP22 monoclonal antibody. The purified fusion protein is administered intranodally at a rate of 10 to 100 pg per day for seven days, followed by seven days rest. An initial treatment of 3-8 cycles are conducted.
[0138) Further, the present invention can utilize various aspects of the following: U.S.
Patent Application Nos. 09/380,534, filed on September 1, 1999, entitled A
METHOD OF
INDUCING A CTL RESPONSE; 09/776,232, filed on February 2, 2001, entitled METHOD OF
INDUCING A CTL RESPONSE; 09/715,835, filed on November 16, 2000, entitled AVOmANCE
OF UNDESIRABLE REPLICATION INTERMEDIATES IN PLASMID PROPOGATION;
09/999,186, filed on November 7, 2001, entitled METHODS OF COMMERCIALIZING AN
ANTIGEN; and Provisional U.S. Patent Application No 60/274,063, filed on March 7, 2001, entitled ANTI-NEOVASCULAR VACCINES FOR CANCER.
Table 11 Partial listine of SEO ID NOS.
1 ELAGIGILTV melan-A 26-35 A27L
2 Melan -A rotein Accession number: NP
3 T osinase rotein Accession number: P14679 4 MLLAVLYCLELAGIGILTVYMDGTMSQVGILT pMA2M expression product VILGVLLLIGCWYCRRRNGYRALMDKSLHVG
TQCALTRRCPQEGFDHRDSKVSLQEKNCEPV
MLLAVLYCLELAGIGILTVYMDGTMSQV Liberation or substrate sequence for SEQ m NO. 1 from MA2M
6 MLLAVLYCL t osinase 1-9 7 YMDGTMSQV ' t osinase 369-377 8 EAAGIGILTV melan-A 26-35 cttaagccaccatgttactagctgttttgtactgcctggaactpM~M insert agcagggatcggcatattgacagtgtatatgga tggaacaatgtcccaggtaggaattctgacagtgatcctggga gtcttactgctcatcggctgttggtattgtaga agacgaaatggatacagagccttgatggataaaagtcttcatg ttggcactcaatgtgccttaacaagaagatgcc cacaagaagggtttgatcatcgggacagcaaagtgtctcttca agagaaaaactgtgaacctgtgtagtgagcggc cgc MVLYCLELAGIGILTVYMDGTAVLYCLELAGI Epitope array from pVAXM2 ~ and _77_ GILTVYMDGTMLAVLYCLELAGIGILTVYMD pVAXMI
GTMSLLAVLYCLELAGIGILTV
11 NY-ESO-1 rotein Accession number: P78358 16 AVLYCL t rosinase 4-9 17 MSLLMWITQCKASEKIFYVRCGARGPESRLLE pN157 expression product FYLAMPFATPMEAELARRSLAQDAPPLPVPGV
LLKEFTV SGNILTIRLTAADHRQLQLSISSCLQ
LSLLMWITQCFLPVFLA PPSGQRR
18 MSLLMWITQCKASEKIFYV liberation or substrate sequence for SE ID NO. 12 from N157 19 cttaagccaccatgtccctgttgatgtggatcacgcagtgcaa~ge~ fOrpN157 agcttcggagaaaatcttctacgtacggtgcgg tgccagggggccggagagccgcctgcttgagttctacctcgcc atgcctttcgcgacacccatggaagcagagctg gcccgcaggagcctggcccaggatgccccaccgcttcccgtgc caggggtgcttctgaaggagttcactgtgtccg gcaacatactgactatccgactgactgctgcagaccaccgcca actgcagctctccatcagctcctgtctccagca gctttccctgttgatgtggatcacgcagtgctttctgcccgtg tttttggctcagcctccctcagggcagaggcgc tagtgagaattc 20 MSLLMWITQCKASEKIFYVGLPSIPVHPIGLPSIpBPL expression product PVHPIKASEKIFYVSLLMWITQCKASEKIFYVK
ASEKIFYVRCGARGPESRLLEFYLAMPFATPM
EAELARRSLAQDAPPLPVPGVLLKEFTVSGNIL, TIRL,TAADHRQLQLSISSCLQQLSLLMWITQCF
LPVFLA PPSGQRR
21 atgtccctgttgatgtggatcacgcagtgcaaagcttcggagap$PLInSertCOdlngreglOri aaatcttctatgtgggtcttccaagtattcctg ttcatccaattggtcttccaagtattcctgttcatccaattaa agcttcggagaaaatcttctatgtgtccctgtt gatgtggatcacgcagtgcaaagcttcggagaaaatcttctat gtgaaagcttcggagaaaatcttctacgtacgg tgcggtgccagggggccggagagccgcctgcttgagttctacc tcgccatgcctttcgcgacacccatggaagcag agctggcccgcaggagcctggcccaggatgccccaccgcttcc cgtgccaggggtgcttctgaaggagttcactgt gtccggcaacatactgactatccgactgactgctgcagaccac cgccaactgcagctctccatcagctcctgtctc cagcagctttccctgttgatgtggatcacgcagtgctttctgc ccgtgtttttggctcagcctccctcagggcaga ggcgctagtga 22 IKASEKIFYVSLLMWITQCKASEKIFYVK Substrate in Fig. 6 23 VMTKLGFKV SSX-457_65 24 RQIYVAAFTV PSMA73o-739 25 AQIPEKIQKAFDDIAKYFSKEEWEKMKASEKIFSSX-2 ~ 5_t g3 YVYMKRKYEAMTKLGFKATLPPFMCNKRAE
DFQGNDLDNDPNRGNQVERPQMTFGRLQGIS
PKIMPKKPAEEGNDSEEVPEASGPQNDGKELC
PPGKPTTSEKIHERSGPKRGEHAWTHRLRERK
LVIYEEISDP
_78_ 26 MVMTKLGFKVKASEKIFYVRQIYVAAFTV CTLS1/pCBPexpressionproduct GLPSIPVHPITQCFLPVFLVMTKLGFKVRQIYV
AAFTVKASEKIFYVAQIPEKIQKAFDDIAKYFS
KEEWEKMKASEKIFYVYMKRKYEAMTKLGF
KATLPPFMCNKRAEDFQGNDLDNDPNRGNQ
VERPQMTFGRLQGISPKIMPKKPAEEGNDSEE
VPEASGPQNDGKELCPPGKPTTSEKIHERSGPK
RGEHA W THRLRERKQLV IYEEISDP
27 MAQIPEKIQKAFDDIAKYFSKEEWEKMKASE CTLS2 expression product KIFYVYMKRKYEAMTKLGFKATLPPFMCNKR
AEDFQGNDLDNDPNRGNQVERPQMTFGRLQ
GISPKIMPKKPAEEGNDSEEVPEASGPQNDGK
ELCPPGKPTTSEKIHERSGPKRGEHAWTHRLR
ERKQLVIYEEISDPVMTKLGFKVKASEKIFYV
RQIYVAAFTVGLPSIPVHPITQCFLPVFLVMTK
LGFKVRQIYVAAFTVKASEKIFYV
28 MVMTKLGFKVKASEKIFYVRQIYVAAFTV CTLS3 expression product GLPSIPVHPIAQIPEKIQKAFDDIAKYFSKEEWE
KMKASEKIFYV YMKRKYEAMTKLGFKATLPP
FMCNKRAEDFQGNDLDNDPNRGNQVERPQM
TFGRLQGISPKIMPKKPAEEGNDSEEVPEASGP
QNDGKELCPPGKPTTSEKIHERSGPKRGEHAW
THRLRERK LVIYEEISDP
29 MAQIPEKIQKAFDDIAKYFSKEEWEKMKASE CTLS4 expressipn product KIFYV YMKRKYEAMTKLGFKATLPPFMCNKR
AEDFQGNDLDNDPNRGNQVERPQMTFGRLQ
GISPKIMPKKPAEEGNDSEEVPEASGPQNDGK
ELCPPGKPTTSEKIHERSGPKRGEHAWTHRLR
ERKQLVIYEEISDPTQCFLPVFLVMTKLGFKVR
QIYVAAFTVKASEKIFYV
30 atggtcatgactaaactaggtttcaaggtcaaagcttcggagapCBP Insert COdlrig region aaatcttctatgtgagacagatttatgttgcag ccttcacagtgggtcttccaagtattcctgttcatccaattac gcagtgctttctgcccgtgtttttggtcatgac taaactaggtttcaaggtcagacagatttatgttgcagccttc acagtgaaagcttcggagaaaatcttctacgta gctcaaataccagagaagatccaaaaggccttcgatgatattg ccaaatacttctctaaggaagagtgggaaaaga tgaaagcctcggagaaaatcttctatgtgtatatgaagagaaa gtatgaggctatgactaaactaggtttcaaggc caccctcccacctttcatgtgtaataaacgggccgaagacttc caggggaatgatttggataatgaccctaaccgt gggaatcaggttgaacgtcctcagatgactttcggcaggctcc agggaatctccccgaagatcatgcccaagaagc cagcagaggaaggaaatgattcggaggaagtgccagaagcatc tggcccacaaaatgatgggaaagagctgtgccc cccgggaaaaccaactacctctgagaagattcacgagagatct ggacccaaaaggggggaacatgcctggacccac agactgcgtgagagaaaacagctggtgatttatgaagagatca gcgacccttagtga 31 RQIYVAAFTVKASEKIFYVAQIPEKIQK Fig. 8 substrate/ CTLS1-2 32 FLPWIIRLFL T~2o7-2~5 33 MLLAVLYCLLWSFQTSAFLPWHRLFLMLLAV CTLT2/pMEL expression product LYCLLWSF TSAFLPWHRLFLMLLAVLYCLL
WSFQTSAFLPWHRLFLMLLAVLYCLLWSFQT
SAFLP WHRLFL
34 atgctcctggctgttttgtactgcctgctgtggagtttccagaCTLT2/pMEL insert coding region cctccgcttttctgccttggcatagactcttct tgatgctcctggctgttttgtactgcctgctgtggagtttcca gacctccgcttttctgccttggcatagactctt cttgatgctcctggctgttttgtactgcctgctgtggagtttc cagacctccgcttttctgccttggcatagactc ttcttgatgctcctggctgttttgtactgcctgctgtggagtt tccagacctccgcttttctgccttggcatagac tcttcttgtagtga 35 MELAN-A cDNA Accession number: NM
36 T rosinase eDNA Accession number: NM
37 NY-ESO-1 cDNA Accession number: U87459 38 PSMA rotein Accession number: NP
39 PSMA cDNA Accession number: NM
40 SSX-2 rotein Accession number: NP
41 SSX-2 cDNA Accession number: NM
42 atgacctctcgccgctccgtgaagtcgggtccgcgggaggttccgcgcFrom accession number:
gatgagtacgaggatctgtactacaccccgtcttcaggtatggcgagtccHerpes Simplex virus cgatagtccgcctgacacctcccgccgtggcgccctacagacacgctccoding sequence (VP22) gcgccagaggggcgaggtccgtttcgtccagtacgacgagtcggattat gccctctacgggggctcgtcatccgaagacgacgaacacccggaggt cccccggacgcggcgtcccgtttccggggcggttttgtccggcccggg gcctgcgcgggcgcctccgccacccgctgggtccggaggggccgga cgcacacccaccaccgccccccgggccccccgaacccagcgggtgg cgactaaggcccccgcggccccggcggcggagaccacccgcggca ggaaatcggcccagceagaatccgccgcactcccagacgcccccgcg tcgacggcgccaacccgatccaagacacccgcgcaggggctggcca gaaagctgcactttagcaccgcccccccaaaccccgacgcgccatgga ccccccgggtggccggctttaacaagcgcgtcttctgcgccgcggtcg ggcgcctggcggccatgcatgcccggatggcggcggtccagctctgg gacatgtcgcgtccgcgcacagacgaagacctcaacgaactccttggc atcaccaccatccgcgtgacggtctgcgagggcaaaaacctgcttcag cgcgccaacgagttggtgaatccagacgtggtgcaggacgtcgacgcg gccacggcgactcgagggcgttctgcggcgtcgcgccccaccgageg acctcgagccccagcccgctccgcttctcgccccagacggcccgtega 43 MTSRRSVKSGPREVPRDEYEDLYYTPSSGMAS Accession number: P10233 PDSPPDTSRRGALFTQTRSRQRGEVRFVQYDE Herpes Simplex virus SDYALYGGSSSEDDEHPEVPRTRRPVSGAVLS UL49/VP22 protein sequence GPGPARAPPPFTPAGSGGAGRTPTTAPRAPRT
QRVATKAPAAPAAETTRGRKSAQPESAALPD
APASTAPTFTRSKTPAQGLARKLHFSTAPPNP
DAPWTPRVAGFNKRVFCAAVGRLAAMHARM
AAVQLWDFTMSRPRTDEDLNELLGITTIRVTV
CEGKNLLQRANELVNPDVVQDVDAATATRG
RSAASRFTPTERPRAPARSASRPRRPVE
Melan-A mRNA sequence LOCUS NM 005511 1524 by mRNA PRI 14-OCT-2001 DEFINITION Homo Sapiens melan-A (MLANA), mRNA.
VERSION NM 005511.1 GI:5031912 (SEQ ID NO. 2) /translation="MPREDAHFIYGYPKKGHGHSYTTAEEAAGIGILTVILGVLLLIGCWYCRRRNGY
RALMDKSLHV GTQCALTRRCPQEGFDHRDSKV SLQEKNCEPV VPNAPPAYEKLSAEQSPPP
YSP"
(SEQ ID NO. 35) ORIGIN
1 agcagacaga ggactctcat taaggaaggt gtcctgtgcc ctgaccctac aagatgccaa 61 gagaagatgc tcacttcatc tatggttacc ccaagaaggg gcacggccac tcttacacca 121 cggctgaaga ggccgctggg atcggcatcc tgacagtgat cctgggagtc ttactgctca 181 tcggctgttg gtattgtaga agacgaaatg gatacagagc cttgatggat aaaagtcttc 241 atgttggcac tcaatgtgcc ttaacaagaa gatgcccaca agaagggttt gatcatcggg 301 acagcaaagt gtctcttcaa gagaaaaact gtgaacctgt ggttcccaat gctccacctg 361 cttatgagaa actctctgca gaacagtcac caccacctta ttcaccttaa gagccagcga 421 gacacctgag acatgctgaa attatttctc tcacactttt gcttgaattt aatacagaca 481 tctaatgttc tcctttggaa tggtgtagga aaaatgcaag ccatctctaa taataagtca 541 gtgttaaaat tttagtaggt ccgctagcag tactaatcat gtgaggaaat gatgagaaat 601 attaaattgg gaaaactcca tcaataaatg ttgcaatgca tgatactatc tgtgccagag 661 gtaatgttag taaatccatg gtgttatttt ctgagagaca gaattcaagt gggtattctg 721 gggccatcca atttctcttt acttgaaatt tggctaataa caaactagtc aggttttcga 781 accttgaccg acatgaactg tacacagaat tgttccagta ctatggagtg ctcacaaagg 841 atacttttac aggttaagac aaagggttga ctggcctatt tatctgatca agaacatgtc 901 agcaatgtct ctttgtgctc taaaattcta ttatactaca ataatatatt gtaaagatcc 961 tatagctctt tttttttgag atggagtttc gcttttgttg cccaggctgg agtgcaatgg 1021 cgcgatcttg gctcaccata acctccgcct cccaggttca agcaattctc ctgccttagc 1081 ctcctgagta gctgggatta caggcgtgcg ccactatgcc tgactaattt tgtagtttta 1141 gtagagacgg ggtttctcca tgttggtcag gctggtctca aactcctgac ctcaggtgat 1201 ctgcccgcct cagcctccca aagtgctgga attacaggcg tgagccacca cgcctggctg 1261 gatcctatat cttaggtaag acatataacg cagtctaatt acatttcact tcaaggctca 1321 atgctattct aactaatgac aagtattttc tactaaacca gaaattggta gaaggattta 1381 aataagtaaa agctactatg tactgcctta gtgctgatgc ctgtgtactg ccttaaatgt 1441 acctatggca atttagctct cttgggttcc caaatccctc tcacaagaat gtgcagaaga 1501 aatcataaag gatcagagat tctg Tyrosinase m)tNA sequence LOCUS NM 000372 1964 by mRNA PRI 31-OCT-2000 DEFINITION Homo Sapiens tyrosinase (oculocutaneous albinism IA) (TYR), mRNA.
VERSION NM 000372.1 GI:4507752 (SEQ ID NO. 3) /translation="MLLAVLYCLLWSFQTSAGHFPRACV SSKNLMEKECCPPW SGDRS
PCGQLSGRGSCQNIL,LSNAPLGPQFPFTGVDDRESWPSVFYNRTCQCSGNFMGFNCGNCKFG
FWGPNCTERRLLVRRNIFDLSAPEKDKFFAYLTLAKHTISSDYVIPIGTYGQMKNGSTPMFND
INIYDLFV WMHYYV SMDALLGGSEIWRD>DFAHEAPAFLPWHRLFLLRWEQEIQKLTGDENF
TIPYWDWRDAEKCDICTDEYMGGQHPTNPNLLSPASFFSSWQIVCSRLEEYNSHQSLCNGTP
EGPLRRNPGNHDKSRTPRLPSSADVEFCLSLTQYESGSMDKAANFSFRNTLEGFASPLTGIAD
ASQSSMHNALHIYMNGTMSQVQGSANDPIFLLHHAFVDSIFEQWLRRHRPLQEVYPEANAPI
GHNRESYMVPFIPLYRNGDFFISSKDLGYDYSYLQDSDPDSFQDYIKSYLEQASRIWSWLLGA
AMVGAVLTALLAGLVSLLCRHKRKQLP EEKQPLLMEKEDYHSLYQSHL"
(SEQ ID NO. 36) ORIGIN
1 atcactgtag tagtagctgg aaagagaaat ctgtgactcc aattagccag ttcctgcaga 61 ccttgtgagg actagaggaa gaatgctcct ggctgttttg tactgcctgc tgtggagttt 121 ccagacctcc gctggccatt tccctagagc ctgtgtctcc tctaagaacc tgatggagaa 181 ggaatgctgt ccaccgtgga gcggggacag gagtccctgt ggccagcttt caggcagagg 241 ttcctgtcag aatatccttc tgtccaatgc accacttggg cctcaatttc ccttcacagg 301 ggtggatgac cgggagtcgt ggccttccgt cttttataat aggacctgcc agtgctctgg 361 caacttcatg ggattcaact gtggaaactg caagtttggc ttttggggac caaactgcac 421 agagagacga ctcttggtga gaagaaacat cttcgatttg agtgccccag agaaggacaa 481 attttttgcc tacctcactt tagcaaagca taccatcagc tcagactatg tcatccccat 541 agggacctat ggccaaatga aaaatggatc aacacccatg tttaacgaca tcaatattta 601 tgacctcttt gtctggatgc attattatgt gtcaatggat gcactgcttg ggggatctga 661 aatctggaga gacattgatt ttgcccatga agcaccagct tttctgcctt ggcatagact 721 cttcttgttg cggtgggaac aagaaatcca gaagctgaca ggagatgaaa acttcactat 781 tccatattgg gactggcggg atgcagaaaa gtgtgacatt tgcacagatg agtacatggg 841 aggtcagcac cccacaaatc ctaacttact cagcccagca tcattcttct cctcttggca 901 gattgtctgt agccgattgg aggagtacaa cagccatcag tctttatgca atggaacgcc 961 cgagggacct ttacggcgta atcctggaaa ccatgacaaa tccagaaccc caaggctccc 1021 ctcttcagct gatgtagaat tttgcctgag tttgacccaa tatgaatctg gttccatgga 1081 taaagctgcc aatttcagct ttagaaatac actggaagga tttgctagtc cacttactgg 1141 gatagcggat gcctctcaaa gcagcatgca caatgccttg cacatctata tgaatggaac 1201 aatgtcccag gtacagggat ctgccaacga tcctatcttc cttcttcacc atgcatttgt 1261 tgacagtatt tttgagcagt ggctccgaag gcaccgtcct cttcaagaag tttatccaga 1321 agccaatgca cccattggac ataaccggga atcctacatg gttcctttta taccactgta 1381 cagaaatggt gatttcttta tttcatccaa agatctgggc tatgactata gctatctaca 1441 agattcagac ccagactctt ttcaagacta cattaagtcc tatttggaac aagcgagtcg 1501 gatctggtca tggctccttg gggcggcgat ggtaggggcc gtcctcactg ccctgctggc 1561 agggcttgtg agcttgctgt gtcgtcacaa gagaaagcag cttcctgaag aaaagcagcc 1621 actcctcatg gagaaagagg attaccacag cttgtatcag agccatttat aaaaggctta 1681 ggcaatagag tagggccaaa aagcctgacc tcactctaac tcaaagtaat gtccaggttc 1741 ccagagaata tctgctggta tttttctgta aagaccattt gcaaaattgt aacctaatac 1801 aaagtgtagc cttcttccaa ctcaggtaga acacacctgt ctttgtcttg ctgttttcac 1861 tcagcccttt taacattttc ccctaagccc atatgtctaa ggaaaggatg ctatttggta 1921 atgaggaact gttatttgta tgtgaattaa agtgctctta tttt NY-ESO-1 mRNA sequence LOCUS HSU87459 752 by mRNA PRI 22-DEC-1999 DEFINITION Human autoimmunogenic cancer/testis antigen NY-ESO-1 mRNA, complete cds.
VERSION U87459.1 GI:1890098 (SEQ ID NO. 11) /translation="MQAEGRGTGGSTGDADGPGGPGII'DGPGGNAGGPGEAGATGGRGPRGAGAAR
ASGPGGGAPRGPHGGAASGLNGCCRCGARGPESRLLEFYLAMPFATPMEAELARRSLAQDA
PPLPVPGVLLKEFTVSGNILTIRLTAADHRQLQLSISSCLQQLSLLM
WITQCFLPVFLAQPPSGQRR"
(SEQ ID NO. 37) ORIGIN
1 atcctcgtgg gccctgacct tctctctgag agccgggcag aggctccgga gccatgcagg 61 ccgaaggccg gggcacaggg ggttcgacgg gcgatgctga tggcccagga ggccctggca 121 ttcctgatgg cccagggggc aatgctggcg gcccaggaga ggcgggtgcc acgggcggca 181 gaggtccccg gggcgcaggg gcagcaaggg cctcggggcc gggaggaggc gccccgcggg 241 gtccgcatgg cggcgcggct tcagggctga atggatgctg cagatgcggg gccagggggc 301 cggagagccg cctgcttgag ttctacctcg ccatgccttt cgcgacaccc atggaagcag 361 agctggcccg caggagcctg gcccaggatg ccccaccgct tcccgtgcca ggggtgcttc 421 tgaaggagtt cactgtgtcc ggcaacatac tgactatccg actgactgct gcagaccacc 481 gccaactgca gctctccatc agctcctgtc tccagcagct ttccctgttg atgtggatca 541 cgcagtgctt tctgcccgtg tttttggctc agcctccctc agggcagagg cgctaagccc 601 agcctggcgc cccttcctag gtcatgcctc ctcccctagg gaatggtccc agcacgagtg 661 gccagttcat tgtgggggcc tgattgtttg tcgctggagg aggacggctt acatgtttgt 721 ttctgtagaa aataaaactg agctacgaaa as PSMA cDNA sequence LOCUS NM 004476 2653 by mRNA PRI O1-NOV-2000 DEFINITION Homo Sapiens folate hydrolase (prostate-specific membrane antigen) 1 (FOLH 1 ), mRNA.
VERSION NM 004476.1 GI:4758397 (SEQ 1D NO. 38) /translation="MWNLLHETDSAVATARRPRWLCAGALVLAGGFFLLGFLFGWFIKSSNEATNIT
PKHNMKAFLDELKAENIKKFLYNFTQIPHLAGTEQNFQLAKQIQSQWKEFGLDSVELAHYD
VLLSYPNKTHPNYISIlNEDGNEIFNTSLFEPPPPGYENVSDIVPPFSAFSPQGMPEGDLVYVNY
ARTEDFFKLERDMKINCSGKIVIARYGKVFRGNKVKNAQLAGAKGVILYSDPADYFAPGVK
SYPDGWNLPGGGVQRGNILNLNGAGDPLTPGYPANEYAYRRGIAEAVGLPSIPVHPIGYYDA
QKLLEKMGGSAPPDSSWRGSLKVPYNVGPGFTGNFSTQKVKMHIHSTNEVTRIYNVIGTLRG
AVEPDRYVILGGH RDSWVFGGIDPQSGAAVVHEIVRSFGTLKKEGWRPRRTILFASWDAEEF
GLLGSTEWAEENSRLLQERGVAYINADSSIEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGF
EGKSLYESWTKKSPSPEFSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNWETNKFSGYPL
YHSVYETYELVEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKYADKIY
SISMKHPQEMKTYSV SFDSLFSAVKNFTEIASKFSERLQDFDKSNPIVLRMMNDQLMFLERAF
IDPLGLPDRPFYRHVIYAPSSHNKYAGESFPGIYDALFDIESKVDPSKAWGEVKRQIYVAAFT
VQAAAETLSEVA"
(SEQ ID NO. 39) ORIGIN
1 ctcaaaaggg gccggatttc cttctcctgg aggcagatgt tgcctctctc tctcgctcgg 61 attggttcag tgcactctag aaacactgct gtggtggaga aactggaccc caggtctgga 121 gcgaattcca gcctgcaggg ctgataagcg aggcattagt gagattgaga gagactttac 181 cccgccgtgg tggttggagg gcgcgcagta gagcagcagc acaggcgcgg gtcccgggag 241 gccggctctg ctcgcgccga gatgtggaat ctccttcacg aaaccgactc ggctgtggcc 301 accgcgcgcc gcccgcgctg gctgtgcgct ggggcgctgg tgctggcggg tggcttcttt 361 ctcctcggct tcctcttcgg gtggtttata aaatcctcca atgaagctac taacattact 421 ccaaagcata atatgaaagc atttttggat gaattgaaag ctgagaacat caagaagttc 481 ttatataatt ttacacagat accacattta gcaggaacag aacaaaactt tcagcttgca 541 aagcaaattc aatcccagtg gaaagaattt ggcctggatt ctgttgagct agcacattat 601 gatgtcctgt tgtcctaccc aaataagact catcccaact acatctcaat aattaatgaa 661 gatggaaatg agattttcaa cacatcatta tttgaaccac ctcctccagg atatgaaaat 721 gtttcggata ttgtaccacc tttcagtgct ttctctcctc aaggaatgcc agagggcgat 781 ctagtgtatg ttaactatgc acgaactgaa gacttcttta aattggaacg ggacatgaaa 841 atcaattgct ctgggaaaat tgtaattgcc agatatggga aagttttcag aggaaataag 901 gttaaaaatg cccagctggc aggggccaaa ggagtcattc tctactccga ccctgctgac 961 tactttgctc ctggggtgaa gtcctatcca gatggttgga atcttcctgg aggtggtgtc 1021 cagcgtggaa atatcctaaa tctgaatggt gcaggagacc ctctcacacc aggttaccca 1081 gcaaatgaat atgcttatag gcgtggaatt gcagaggctg ttggtcttcc aagtattcct 1141 gttcatccaa ttggatacta tgatgcacag aagctcctag aaaaaatggg tggctcagca 1201 ccaccagata gcagctggag aggaagtctc aaagtgccct acaatgttgg acctggcttt 1261 actggaaact tttctacaca aaaagtcaag atgcacatcc actctaccaa tgaagtgaca 1321 agaatttaca atgtgatagg tactctcaga ggagcagtgg aaccagacag atatgtcatt 1381 ctgggaggtc accgggactc atgggtgttt ggtggtattg accctcagag tggagcagct 1441 gttgttcatg aaattgtgag gagctttgga acactgaaaa aggaagggtg gagacctaga 1501 agaacaattt tgtttgcaag ctgggatgca gaagaatttg gtcttcttgg ttctactgag 1561 tgggcagagg agaattcaag actccttcaa gagcgtggcg tggcttatat taatgctgac 1621 tcatctatag aaggaaacta cactctgaga gttgattgta caccgctgat gtacagcttg 1681 gtacacaacc taacaaaaga gctgaaaagc cctgatgaag gctttgaagg caaatctctt 1741 tatgaaagtt ggactaaaaa aagtccttcc ccagagttca gtggcatgcc caggataagc 1801 aaattgggat ctggaaatga ttttgaggtg ttcttccaac gacttggaat tgcttcaggc 1861 agagcacggt atactaaaaa ttgggaaaca aacaaattca gcggctatcc actgtatcac 1921 agtgtctatg aaacatatga gttggtggaa aagttttatg atccaatgtt taaatatcac 1981 ctcactgtgg cccaggttcg aggagggatg gtgtttgagc tagccaattc catagtgctc 2041 ccttttgatt gtcgagatta tgctgtagtt ttaagaaagt atgctgacaa aatctacagt 2101 atttctatga aacatccaca ggaaatgaag acatacagtg tatcatttga ttcacttttt 2161 tctgcagtaa agaattttac agaaattgct tccaagttca gtgagagact ccaggacttt 2221 gacaaaagca acccaatagt attaagaatg atgaatgatc aactcatgtt tctggaaaga 2281 gcatttattg atccattagg gttaccagac aggccttttt ataggcatgt catctatgct 2341 ccaagcagcc acaacaagta tgcaggggag tcattcccag gaatttatga tgctctgttt 2401 gatattgaaa gcaaagtgga cccttccaag gcctggggag aagtgaagag acagatttat 2461 gttgcagcct tcacagtgca ggcagctgca gagactttga gtgaagtagc ctaagaggat 2521 tctttagaga atccgtattg aatttgtgtg gtatgtcact cagaaagaat cgtaatgggt 2581 atattgataa attttaaaat tggtatattt gaaataaagt tgaatattat atataaaaaa 2641 aaaaaaaaaa aaa NM 003147 Homo Sapiens synovial sarcoma, X breakpoint 2 (SSX2), ml2NA
LOCUS NM-003147 766 by mRNA PRI 14-MAR-2001 DEFINITION Homo Sapiens synovial sarcoma, X breakpoint 2 (SSX2), mRNA.
ACCESSION NM_003147 VERSION NM 003147.1 GI:10337582 SEQ ID NO. 40 /translation=~~MNGDDAFARRPTVGAQIPEKIQKAFDDIAKYFSKEEWEKMKASE
KIFYVYMKRKYEAMTKLGFKATLPPFMCNKRAEDFQGNDLDNDPNRGNQVERPQMTFG
RLQGISPKIMPKKPAEEGNDSEEVPEASGPQNDGKELCPPGKPTTSEKIHERSGPKRG
EHAWTHRLRERKQLVIYEEISDPEEDDE"
1 ctctctttcg attcttccat actcagagta cgcacggtct gattttctct ttggattctt 61 ccaaaatcag agtcagactg ctcccggtgc catgaacgga gacgacgcct ttgcaaggag 121 acccacggtt ggtgctcaaa taccagagaa gatccaaaag gccttcgatg atattgccaa 181 atacttctct aaggaagagt gggaaaagat gaaagcctcg gagaaaatct tctatgtgta 241 tatgaagaga aagtatgagg ctatgactaa actaggtttc aaggccaccc tcccaccttt 301 catgtgtaat aaacgggccg aagacttcca ggggaatgat ttggataatg accctaaccg 361 tgggaatcag gttgaacgtc ctcagatgac tttcggcagg ctccagggaa tctccccgaa 421 gatcatgccc aagaagccag cagaggaagg aaatgattcg gaggaagtgc cagaagcatc 481 tggcccacaa aatgatggga aagagctgtg ccccccggga aaaccaacta cctctgagaa 541 gattcacgag agatctggac ccaaaagggg ggaacatgcc tggacccaca gactgcgtga 601 gagaaaacag ctggtgattt atgaagagat cagcgaccct gaggaagatg acgagtaact 661 cccctcaggg atacgacaca tgcccatgat gagaagcaga acgtggtgac ctttcacgaa 721 catgggcatg gctgcggacc cctcgtcatc aggtgcatag caagtg
gatgagtacgaggatctgtactacaccccgtcttcaggtatggcgagtccHerpes Simplex virus cgatagtccgcctgacacctcccgccgtggcgccctacagacacgctccoding sequence (VP22) gcgccagaggggcgaggtccgtttcgtccagtacgacgagtcggattat gccctctacgggggctcgtcatccgaagacgacgaacacccggaggt cccccggacgcggcgtcccgtttccggggcggttttgtccggcccggg gcctgcgcgggcgcctccgccacccgctgggtccggaggggccgga cgcacacccaccaccgccccccgggccccccgaacccagcgggtgg cgactaaggcccccgcggccccggcggcggagaccacccgcggca ggaaatcggcccagceagaatccgccgcactcccagacgcccccgcg tcgacggcgccaacccgatccaagacacccgcgcaggggctggcca gaaagctgcactttagcaccgcccccccaaaccccgacgcgccatgga ccccccgggtggccggctttaacaagcgcgtcttctgcgccgcggtcg ggcgcctggcggccatgcatgcccggatggcggcggtccagctctgg gacatgtcgcgtccgcgcacagacgaagacctcaacgaactccttggc atcaccaccatccgcgtgacggtctgcgagggcaaaaacctgcttcag cgcgccaacgagttggtgaatccagacgtggtgcaggacgtcgacgcg gccacggcgactcgagggcgttctgcggcgtcgcgccccaccgageg acctcgagccccagcccgctccgcttctcgccccagacggcccgtega 43 MTSRRSVKSGPREVPRDEYEDLYYTPSSGMAS Accession number: P10233 PDSPPDTSRRGALFTQTRSRQRGEVRFVQYDE Herpes Simplex virus SDYALYGGSSSEDDEHPEVPRTRRPVSGAVLS UL49/VP22 protein sequence GPGPARAPPPFTPAGSGGAGRTPTTAPRAPRT
QRVATKAPAAPAAETTRGRKSAQPESAALPD
APASTAPTFTRSKTPAQGLARKLHFSTAPPNP
DAPWTPRVAGFNKRVFCAAVGRLAAMHARM
AAVQLWDFTMSRPRTDEDLNELLGITTIRVTV
CEGKNLLQRANELVNPDVVQDVDAATATRG
RSAASRFTPTERPRAPARSASRPRRPVE
Melan-A mRNA sequence LOCUS NM 005511 1524 by mRNA PRI 14-OCT-2001 DEFINITION Homo Sapiens melan-A (MLANA), mRNA.
VERSION NM 005511.1 GI:5031912 (SEQ ID NO. 2) /translation="MPREDAHFIYGYPKKGHGHSYTTAEEAAGIGILTVILGVLLLIGCWYCRRRNGY
RALMDKSLHV GTQCALTRRCPQEGFDHRDSKV SLQEKNCEPV VPNAPPAYEKLSAEQSPPP
YSP"
(SEQ ID NO. 35) ORIGIN
1 agcagacaga ggactctcat taaggaaggt gtcctgtgcc ctgaccctac aagatgccaa 61 gagaagatgc tcacttcatc tatggttacc ccaagaaggg gcacggccac tcttacacca 121 cggctgaaga ggccgctggg atcggcatcc tgacagtgat cctgggagtc ttactgctca 181 tcggctgttg gtattgtaga agacgaaatg gatacagagc cttgatggat aaaagtcttc 241 atgttggcac tcaatgtgcc ttaacaagaa gatgcccaca agaagggttt gatcatcggg 301 acagcaaagt gtctcttcaa gagaaaaact gtgaacctgt ggttcccaat gctccacctg 361 cttatgagaa actctctgca gaacagtcac caccacctta ttcaccttaa gagccagcga 421 gacacctgag acatgctgaa attatttctc tcacactttt gcttgaattt aatacagaca 481 tctaatgttc tcctttggaa tggtgtagga aaaatgcaag ccatctctaa taataagtca 541 gtgttaaaat tttagtaggt ccgctagcag tactaatcat gtgaggaaat gatgagaaat 601 attaaattgg gaaaactcca tcaataaatg ttgcaatgca tgatactatc tgtgccagag 661 gtaatgttag taaatccatg gtgttatttt ctgagagaca gaattcaagt gggtattctg 721 gggccatcca atttctcttt acttgaaatt tggctaataa caaactagtc aggttttcga 781 accttgaccg acatgaactg tacacagaat tgttccagta ctatggagtg ctcacaaagg 841 atacttttac aggttaagac aaagggttga ctggcctatt tatctgatca agaacatgtc 901 agcaatgtct ctttgtgctc taaaattcta ttatactaca ataatatatt gtaaagatcc 961 tatagctctt tttttttgag atggagtttc gcttttgttg cccaggctgg agtgcaatgg 1021 cgcgatcttg gctcaccata acctccgcct cccaggttca agcaattctc ctgccttagc 1081 ctcctgagta gctgggatta caggcgtgcg ccactatgcc tgactaattt tgtagtttta 1141 gtagagacgg ggtttctcca tgttggtcag gctggtctca aactcctgac ctcaggtgat 1201 ctgcccgcct cagcctccca aagtgctgga attacaggcg tgagccacca cgcctggctg 1261 gatcctatat cttaggtaag acatataacg cagtctaatt acatttcact tcaaggctca 1321 atgctattct aactaatgac aagtattttc tactaaacca gaaattggta gaaggattta 1381 aataagtaaa agctactatg tactgcctta gtgctgatgc ctgtgtactg ccttaaatgt 1441 acctatggca atttagctct cttgggttcc caaatccctc tcacaagaat gtgcagaaga 1501 aatcataaag gatcagagat tctg Tyrosinase m)tNA sequence LOCUS NM 000372 1964 by mRNA PRI 31-OCT-2000 DEFINITION Homo Sapiens tyrosinase (oculocutaneous albinism IA) (TYR), mRNA.
VERSION NM 000372.1 GI:4507752 (SEQ ID NO. 3) /translation="MLLAVLYCLLWSFQTSAGHFPRACV SSKNLMEKECCPPW SGDRS
PCGQLSGRGSCQNIL,LSNAPLGPQFPFTGVDDRESWPSVFYNRTCQCSGNFMGFNCGNCKFG
FWGPNCTERRLLVRRNIFDLSAPEKDKFFAYLTLAKHTISSDYVIPIGTYGQMKNGSTPMFND
INIYDLFV WMHYYV SMDALLGGSEIWRD>DFAHEAPAFLPWHRLFLLRWEQEIQKLTGDENF
TIPYWDWRDAEKCDICTDEYMGGQHPTNPNLLSPASFFSSWQIVCSRLEEYNSHQSLCNGTP
EGPLRRNPGNHDKSRTPRLPSSADVEFCLSLTQYESGSMDKAANFSFRNTLEGFASPLTGIAD
ASQSSMHNALHIYMNGTMSQVQGSANDPIFLLHHAFVDSIFEQWLRRHRPLQEVYPEANAPI
GHNRESYMVPFIPLYRNGDFFISSKDLGYDYSYLQDSDPDSFQDYIKSYLEQASRIWSWLLGA
AMVGAVLTALLAGLVSLLCRHKRKQLP EEKQPLLMEKEDYHSLYQSHL"
(SEQ ID NO. 36) ORIGIN
1 atcactgtag tagtagctgg aaagagaaat ctgtgactcc aattagccag ttcctgcaga 61 ccttgtgagg actagaggaa gaatgctcct ggctgttttg tactgcctgc tgtggagttt 121 ccagacctcc gctggccatt tccctagagc ctgtgtctcc tctaagaacc tgatggagaa 181 ggaatgctgt ccaccgtgga gcggggacag gagtccctgt ggccagcttt caggcagagg 241 ttcctgtcag aatatccttc tgtccaatgc accacttggg cctcaatttc ccttcacagg 301 ggtggatgac cgggagtcgt ggccttccgt cttttataat aggacctgcc agtgctctgg 361 caacttcatg ggattcaact gtggaaactg caagtttggc ttttggggac caaactgcac 421 agagagacga ctcttggtga gaagaaacat cttcgatttg agtgccccag agaaggacaa 481 attttttgcc tacctcactt tagcaaagca taccatcagc tcagactatg tcatccccat 541 agggacctat ggccaaatga aaaatggatc aacacccatg tttaacgaca tcaatattta 601 tgacctcttt gtctggatgc attattatgt gtcaatggat gcactgcttg ggggatctga 661 aatctggaga gacattgatt ttgcccatga agcaccagct tttctgcctt ggcatagact 721 cttcttgttg cggtgggaac aagaaatcca gaagctgaca ggagatgaaa acttcactat 781 tccatattgg gactggcggg atgcagaaaa gtgtgacatt tgcacagatg agtacatggg 841 aggtcagcac cccacaaatc ctaacttact cagcccagca tcattcttct cctcttggca 901 gattgtctgt agccgattgg aggagtacaa cagccatcag tctttatgca atggaacgcc 961 cgagggacct ttacggcgta atcctggaaa ccatgacaaa tccagaaccc caaggctccc 1021 ctcttcagct gatgtagaat tttgcctgag tttgacccaa tatgaatctg gttccatgga 1081 taaagctgcc aatttcagct ttagaaatac actggaagga tttgctagtc cacttactgg 1141 gatagcggat gcctctcaaa gcagcatgca caatgccttg cacatctata tgaatggaac 1201 aatgtcccag gtacagggat ctgccaacga tcctatcttc cttcttcacc atgcatttgt 1261 tgacagtatt tttgagcagt ggctccgaag gcaccgtcct cttcaagaag tttatccaga 1321 agccaatgca cccattggac ataaccggga atcctacatg gttcctttta taccactgta 1381 cagaaatggt gatttcttta tttcatccaa agatctgggc tatgactata gctatctaca 1441 agattcagac ccagactctt ttcaagacta cattaagtcc tatttggaac aagcgagtcg 1501 gatctggtca tggctccttg gggcggcgat ggtaggggcc gtcctcactg ccctgctggc 1561 agggcttgtg agcttgctgt gtcgtcacaa gagaaagcag cttcctgaag aaaagcagcc 1621 actcctcatg gagaaagagg attaccacag cttgtatcag agccatttat aaaaggctta 1681 ggcaatagag tagggccaaa aagcctgacc tcactctaac tcaaagtaat gtccaggttc 1741 ccagagaata tctgctggta tttttctgta aagaccattt gcaaaattgt aacctaatac 1801 aaagtgtagc cttcttccaa ctcaggtaga acacacctgt ctttgtcttg ctgttttcac 1861 tcagcccttt taacattttc ccctaagccc atatgtctaa ggaaaggatg ctatttggta 1921 atgaggaact gttatttgta tgtgaattaa agtgctctta tttt NY-ESO-1 mRNA sequence LOCUS HSU87459 752 by mRNA PRI 22-DEC-1999 DEFINITION Human autoimmunogenic cancer/testis antigen NY-ESO-1 mRNA, complete cds.
VERSION U87459.1 GI:1890098 (SEQ ID NO. 11) /translation="MQAEGRGTGGSTGDADGPGGPGII'DGPGGNAGGPGEAGATGGRGPRGAGAAR
ASGPGGGAPRGPHGGAASGLNGCCRCGARGPESRLLEFYLAMPFATPMEAELARRSLAQDA
PPLPVPGVLLKEFTVSGNILTIRLTAADHRQLQLSISSCLQQLSLLM
WITQCFLPVFLAQPPSGQRR"
(SEQ ID NO. 37) ORIGIN
1 atcctcgtgg gccctgacct tctctctgag agccgggcag aggctccgga gccatgcagg 61 ccgaaggccg gggcacaggg ggttcgacgg gcgatgctga tggcccagga ggccctggca 121 ttcctgatgg cccagggggc aatgctggcg gcccaggaga ggcgggtgcc acgggcggca 181 gaggtccccg gggcgcaggg gcagcaaggg cctcggggcc gggaggaggc gccccgcggg 241 gtccgcatgg cggcgcggct tcagggctga atggatgctg cagatgcggg gccagggggc 301 cggagagccg cctgcttgag ttctacctcg ccatgccttt cgcgacaccc atggaagcag 361 agctggcccg caggagcctg gcccaggatg ccccaccgct tcccgtgcca ggggtgcttc 421 tgaaggagtt cactgtgtcc ggcaacatac tgactatccg actgactgct gcagaccacc 481 gccaactgca gctctccatc agctcctgtc tccagcagct ttccctgttg atgtggatca 541 cgcagtgctt tctgcccgtg tttttggctc agcctccctc agggcagagg cgctaagccc 601 agcctggcgc cccttcctag gtcatgcctc ctcccctagg gaatggtccc agcacgagtg 661 gccagttcat tgtgggggcc tgattgtttg tcgctggagg aggacggctt acatgtttgt 721 ttctgtagaa aataaaactg agctacgaaa as PSMA cDNA sequence LOCUS NM 004476 2653 by mRNA PRI O1-NOV-2000 DEFINITION Homo Sapiens folate hydrolase (prostate-specific membrane antigen) 1 (FOLH 1 ), mRNA.
VERSION NM 004476.1 GI:4758397 (SEQ 1D NO. 38) /translation="MWNLLHETDSAVATARRPRWLCAGALVLAGGFFLLGFLFGWFIKSSNEATNIT
PKHNMKAFLDELKAENIKKFLYNFTQIPHLAGTEQNFQLAKQIQSQWKEFGLDSVELAHYD
VLLSYPNKTHPNYISIlNEDGNEIFNTSLFEPPPPGYENVSDIVPPFSAFSPQGMPEGDLVYVNY
ARTEDFFKLERDMKINCSGKIVIARYGKVFRGNKVKNAQLAGAKGVILYSDPADYFAPGVK
SYPDGWNLPGGGVQRGNILNLNGAGDPLTPGYPANEYAYRRGIAEAVGLPSIPVHPIGYYDA
QKLLEKMGGSAPPDSSWRGSLKVPYNVGPGFTGNFSTQKVKMHIHSTNEVTRIYNVIGTLRG
AVEPDRYVILGGH RDSWVFGGIDPQSGAAVVHEIVRSFGTLKKEGWRPRRTILFASWDAEEF
GLLGSTEWAEENSRLLQERGVAYINADSSIEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGF
EGKSLYESWTKKSPSPEFSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNWETNKFSGYPL
YHSVYETYELVEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKYADKIY
SISMKHPQEMKTYSV SFDSLFSAVKNFTEIASKFSERLQDFDKSNPIVLRMMNDQLMFLERAF
IDPLGLPDRPFYRHVIYAPSSHNKYAGESFPGIYDALFDIESKVDPSKAWGEVKRQIYVAAFT
VQAAAETLSEVA"
(SEQ ID NO. 39) ORIGIN
1 ctcaaaaggg gccggatttc cttctcctgg aggcagatgt tgcctctctc tctcgctcgg 61 attggttcag tgcactctag aaacactgct gtggtggaga aactggaccc caggtctgga 121 gcgaattcca gcctgcaggg ctgataagcg aggcattagt gagattgaga gagactttac 181 cccgccgtgg tggttggagg gcgcgcagta gagcagcagc acaggcgcgg gtcccgggag 241 gccggctctg ctcgcgccga gatgtggaat ctccttcacg aaaccgactc ggctgtggcc 301 accgcgcgcc gcccgcgctg gctgtgcgct ggggcgctgg tgctggcggg tggcttcttt 361 ctcctcggct tcctcttcgg gtggtttata aaatcctcca atgaagctac taacattact 421 ccaaagcata atatgaaagc atttttggat gaattgaaag ctgagaacat caagaagttc 481 ttatataatt ttacacagat accacattta gcaggaacag aacaaaactt tcagcttgca 541 aagcaaattc aatcccagtg gaaagaattt ggcctggatt ctgttgagct agcacattat 601 gatgtcctgt tgtcctaccc aaataagact catcccaact acatctcaat aattaatgaa 661 gatggaaatg agattttcaa cacatcatta tttgaaccac ctcctccagg atatgaaaat 721 gtttcggata ttgtaccacc tttcagtgct ttctctcctc aaggaatgcc agagggcgat 781 ctagtgtatg ttaactatgc acgaactgaa gacttcttta aattggaacg ggacatgaaa 841 atcaattgct ctgggaaaat tgtaattgcc agatatggga aagttttcag aggaaataag 901 gttaaaaatg cccagctggc aggggccaaa ggagtcattc tctactccga ccctgctgac 961 tactttgctc ctggggtgaa gtcctatcca gatggttgga atcttcctgg aggtggtgtc 1021 cagcgtggaa atatcctaaa tctgaatggt gcaggagacc ctctcacacc aggttaccca 1081 gcaaatgaat atgcttatag gcgtggaatt gcagaggctg ttggtcttcc aagtattcct 1141 gttcatccaa ttggatacta tgatgcacag aagctcctag aaaaaatggg tggctcagca 1201 ccaccagata gcagctggag aggaagtctc aaagtgccct acaatgttgg acctggcttt 1261 actggaaact tttctacaca aaaagtcaag atgcacatcc actctaccaa tgaagtgaca 1321 agaatttaca atgtgatagg tactctcaga ggagcagtgg aaccagacag atatgtcatt 1381 ctgggaggtc accgggactc atgggtgttt ggtggtattg accctcagag tggagcagct 1441 gttgttcatg aaattgtgag gagctttgga acactgaaaa aggaagggtg gagacctaga 1501 agaacaattt tgtttgcaag ctgggatgca gaagaatttg gtcttcttgg ttctactgag 1561 tgggcagagg agaattcaag actccttcaa gagcgtggcg tggcttatat taatgctgac 1621 tcatctatag aaggaaacta cactctgaga gttgattgta caccgctgat gtacagcttg 1681 gtacacaacc taacaaaaga gctgaaaagc cctgatgaag gctttgaagg caaatctctt 1741 tatgaaagtt ggactaaaaa aagtccttcc ccagagttca gtggcatgcc caggataagc 1801 aaattgggat ctggaaatga ttttgaggtg ttcttccaac gacttggaat tgcttcaggc 1861 agagcacggt atactaaaaa ttgggaaaca aacaaattca gcggctatcc actgtatcac 1921 agtgtctatg aaacatatga gttggtggaa aagttttatg atccaatgtt taaatatcac 1981 ctcactgtgg cccaggttcg aggagggatg gtgtttgagc tagccaattc catagtgctc 2041 ccttttgatt gtcgagatta tgctgtagtt ttaagaaagt atgctgacaa aatctacagt 2101 atttctatga aacatccaca ggaaatgaag acatacagtg tatcatttga ttcacttttt 2161 tctgcagtaa agaattttac agaaattgct tccaagttca gtgagagact ccaggacttt 2221 gacaaaagca acccaatagt attaagaatg atgaatgatc aactcatgtt tctggaaaga 2281 gcatttattg atccattagg gttaccagac aggccttttt ataggcatgt catctatgct 2341 ccaagcagcc acaacaagta tgcaggggag tcattcccag gaatttatga tgctctgttt 2401 gatattgaaa gcaaagtgga cccttccaag gcctggggag aagtgaagag acagatttat 2461 gttgcagcct tcacagtgca ggcagctgca gagactttga gtgaagtagc ctaagaggat 2521 tctttagaga atccgtattg aatttgtgtg gtatgtcact cagaaagaat cgtaatgggt 2581 atattgataa attttaaaat tggtatattt gaaataaagt tgaatattat atataaaaaa 2641 aaaaaaaaaa aaa NM 003147 Homo Sapiens synovial sarcoma, X breakpoint 2 (SSX2), ml2NA
LOCUS NM-003147 766 by mRNA PRI 14-MAR-2001 DEFINITION Homo Sapiens synovial sarcoma, X breakpoint 2 (SSX2), mRNA.
ACCESSION NM_003147 VERSION NM 003147.1 GI:10337582 SEQ ID NO. 40 /translation=~~MNGDDAFARRPTVGAQIPEKIQKAFDDIAKYFSKEEWEKMKASE
KIFYVYMKRKYEAMTKLGFKATLPPFMCNKRAEDFQGNDLDNDPNRGNQVERPQMTFG
RLQGISPKIMPKKPAEEGNDSEEVPEASGPQNDGKELCPPGKPTTSEKIHERSGPKRG
EHAWTHRLRERKQLVIYEEISDPEEDDE"
1 ctctctttcg attcttccat actcagagta cgcacggtct gattttctct ttggattctt 61 ccaaaatcag agtcagactg ctcccggtgc catgaacgga gacgacgcct ttgcaaggag 121 acccacggtt ggtgctcaaa taccagagaa gatccaaaag gccttcgatg atattgccaa 181 atacttctct aaggaagagt gggaaaagat gaaagcctcg gagaaaatct tctatgtgta 241 tatgaagaga aagtatgagg ctatgactaa actaggtttc aaggccaccc tcccaccttt 301 catgtgtaat aaacgggccg aagacttcca ggggaatgat ttggataatg accctaaccg 361 tgggaatcag gttgaacgtc ctcagatgac tttcggcagg ctccagggaa tctccccgaa 421 gatcatgccc aagaagccag cagaggaagg aaatgattcg gaggaagtgc cagaagcatc 481 tggcccacaa aatgatggga aagagctgtg ccccccggga aaaccaacta cctctgagaa 541 gattcacgag agatctggac ccaaaagggg ggaacatgcc tggacccaca gactgcgtga 601 gagaaaacag ctggtgattt atgaagagat cagcgaccct gaggaagatg acgagtaact 661 cccctcaggg atacgacaca tgcccatgat gagaagcaga acgtggtgac ctttcacgaa 721 catgggcatg gctgcggacc cctcgtcatc aggtgcatag caagtg
Claims (21)
1. A method of identifying a polypeptide suitable for epitope liberation, the method comprising the steps of:
identifying an epitope of interest;
providing a substrate polypeptide sequence comprising the epitope, wherein the substrate polypeptide permits processing by a proteasome;
contacting the substrate polypeptide with a composition comprising the proteasome, under conditions that support processing of the substrate polypeptide by the proteasome; and assaying for liberation of the epitope.
identifying an epitope of interest;
providing a substrate polypeptide sequence comprising the epitope, wherein the substrate polypeptide permits processing by a proteasome;
contacting the substrate polypeptide with a composition comprising the proteasome, under conditions that support processing of the substrate polypeptide by the proteasome; and assaying for liberation of the epitope.
2. The method of claim 1, wherein the epitope is embedded in the substrate polypeptide.
3. The method of claim 1, wherein the epitope is a housekeeping epitope.
4. The method of claim 1, wherein the substrate polypeptide is a synthetic peptide.
5. The method of claim 1, wherein the substrate polypeptide is a fusion protein.
6. The method of claim 1, wherein the contacting step comprises immunization with the substrate polypeptide.
7. The method of claim 1, wherein the substrate polypeptide is encoded by a polynucleotide.
8. The method of claim 7, wherein the contacting step comprises immunization with a vector comprising the polynucleotide.
9. The method of claim 7, wherein the contacting step comprises transforming a cell with a vector comprising the polynucleotide.
10. The method of claim 1, wherein the proteasome processing takes place in vitro.
11. The method of claim 1, wherein the assaying step consists of a technique selected from the group consisting of mass spectrometry, N-terminal pool sequencing, and HPLC.
12. The method of claim 1, wherein the assaying step comprises a T cell target recognition assay.
13. The method of claim 1, wherein the substrate polypeptide further comprises an array of additional epitopes.
14. The method of claim 13, wherein the array comprises a housekeeping and an immune epitope.
15. The method of claim 1, wherein the substrate polypeptide further comprises an array of epitopes and epitope clusters.
16. The method of Claim 1, wherein the proteasome is an immune proteasome.
17. A vector comprising a housekeeping epitope expression cassette, wherein the housekeeping epitope is derived from a target-associated antigen, and wherein the housekeeping epitope is liberatable from a translation product of the cassette by immunoproteasome processing.
18. The vector of claim 17, wherein the expression cassette encodes an array of two or more epitopes or at least one epitope and at least one epitope cluster.
19. The vector of claim 17, wherein the target-associated antigen is an antigen derived from or associated with a tumor or an intracellular parasite.
20. A method of activating a T cell comprising contacting the vector of claim 17 with an APC and contacting said APC with a T cell.
21. A substrate polypeptide comprising a housekeeping epitope wherein the housekeeping epitope can be liberated by immunoproteasome processing in a pAPC.
Applications Claiming Priority (3)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US33696801P | 2001-11-07 | 2001-11-07 | |
US60/336,968 | 2001-11-07 | ||
PCT/US2002/036098 WO2003063770A2 (en) | 2001-11-07 | 2002-11-07 | Expression vectors encoding epitopes of target-associated antigens and methods for their design |
Publications (1)
Publication Number | Publication Date |
---|---|
CA2469738A1 true CA2469738A1 (en) | 2003-08-07 |
Family
ID=27662934
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
CA 2469738 Abandoned CA2469738A1 (en) | 2001-11-07 | 2002-11-07 | Expression vectors encoding epitopes of target-associated antigens and methods for their design |
Country Status (12)
Country | Link |
---|---|
US (3) | US8637305B2 (en) |
EP (2) | EP2314712B1 (en) |
CN (2) | CN1313617C (en) |
AT (1) | ATE494387T1 (en) |
AU (1) | AU2008229722B2 (en) |
CA (1) | CA2469738A1 (en) |
DE (1) | DE60238864D1 (en) |
DK (1) | DK1453471T3 (en) |
ES (1) | ES2358642T3 (en) |
HK (2) | HK1068807A1 (en) |
MX (1) | MXPA04005382A (en) |
WO (1) | WO2003063770A2 (en) |
Families Citing this family (76)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US6136311A (en) | 1996-05-06 | 2000-10-24 | Cornell Research Foundation, Inc. | Treatment and diagnosis of cancer |
US6977074B2 (en) * | 1997-07-10 | 2005-12-20 | Mannkind Corporation | Method of inducing a CTL response |
US9006175B2 (en) | 1999-06-29 | 2015-04-14 | Mannkind Corporation | Potentiation of glucose elimination |
JP4540033B2 (en) | 1999-10-22 | 2010-09-08 | サノフィ パストゥール リミテッド | Methods for inducing and / or enhancing immune responses against tumor antigens |
US20030215425A1 (en) * | 2001-12-07 | 2003-11-20 | Simard John J. L. | Epitope synchronization in antigen presenting cells |
WO2003008537A2 (en) * | 2001-04-06 | 2003-01-30 | Mannkind Corporation | Epitope sequences |
EP2314712B1 (en) * | 2001-11-07 | 2014-01-08 | Mannkind Corporation | Expression vectors encoding epitopes of antigens and methods for their design |
CA2479751C (en) | 2002-03-20 | 2008-06-03 | Trent Poole | Inhalation apparatus |
US7178491B2 (en) * | 2003-06-05 | 2007-02-20 | Caterpillar Inc | Control system and method for engine valve actuator |
DK1635863T3 (en) | 2003-06-17 | 2010-11-22 | Mannkind Corp | Compositions for triggering, enhancing and maintaining immune responses to MHC class-I restricted epitopes for prophylactic or therapeutic purposes |
EP2338506A3 (en) * | 2003-06-17 | 2011-10-12 | Mannkind Corporation | Combinations of tumor-associated antigens for the treatment of various types of cancers |
EP1670509A4 (en) * | 2003-09-03 | 2007-10-31 | Dendritherapeutics Inc | Multiplex vaccines |
US20060159689A1 (en) * | 2004-06-17 | 2006-07-20 | Chih-Sheng Chiang | Combinations of tumor-associated antigens in diagnostics for various types of cancers |
EP1773402A2 (en) * | 2004-06-17 | 2007-04-18 | Mannkind Corporation | Improved efficacy of immunotherapy by integrating diagnostic with therapeutic methods |
JP5166025B2 (en) * | 2004-06-17 | 2013-03-21 | マンカインド コーポレイション | Epitope analog |
US20060008468A1 (en) * | 2004-06-17 | 2006-01-12 | Chih-Sheng Chiang | Combinations of tumor-associated antigens in diagnostics for various types of cancers |
KR101273120B1 (en) | 2004-08-20 | 2013-06-13 | 맨카인드 코포레이션 | Catalysis of diketopiperazine synthesis |
KR101644250B1 (en) | 2004-08-23 | 2016-07-29 | 맨카인드 코포레이션 | Diketopiperazine salts, diketomorpholine salts or diketodioxane salts for drug delivery |
WO2006081007A2 (en) * | 2004-12-16 | 2006-08-03 | Wake Forest University Health Sciences | Use of flagellin in tumor immunotherapy |
EP2351576A1 (en) | 2004-12-29 | 2011-08-03 | Mannkind Corporation | Methods to trigger, maintain and manipulate immune responses by targeted administration of biological response modifiers into lymphoid organs |
JP2008526760A (en) * | 2004-12-29 | 2008-07-24 | マンカインド コーポレイション | Use of a composition containing various tumor-associated antigens as an anticancer vaccine |
CA2592972A1 (en) * | 2004-12-29 | 2006-07-06 | Mannkind Corporation | Methods to bypass cd+4 cells in the induction of an immune response |
US20060165711A1 (en) * | 2004-12-29 | 2006-07-27 | Bot Adrian I | Methods to elicit, enhance and sustain immune responses against MHC class I-restricted epitopes, for prophylactic or therapeutic purposes |
NZ564360A (en) | 2005-06-17 | 2011-03-31 | Mannkind Corp | Immunogenic product comprising a nucleic acid capable of expressing a PRAME epitope and a PSMA epitope and a peptide composition |
MX2007015933A (en) | 2005-06-17 | 2008-04-21 | Mannkind Corp | Methods and compositions to elicit multivalent immune responses against dominant and subdominant epitopes, expressed on cancer cells and tumor stroma. |
EP2371851A3 (en) * | 2005-06-17 | 2012-08-01 | Mannkind Corporation | Epitope analogues |
KR101486397B1 (en) | 2005-09-14 | 2015-01-28 | 맨카인드 코포레이션 | Method of drug formulation based on increasing the affinity of crystalline microparticle surfaces for active agents |
BRPI0707991B8 (en) | 2006-02-22 | 2021-05-25 | Mannkind Corp | methods of preparing a dry powder medicine with an improved pharmaceutical property, said dry powder and using an effective amount of the dry powder |
ATE509033T1 (en) | 2006-03-20 | 2011-05-15 | Univ California | ENGINEERED ANTI-PROSTATE STEM CELL ANTIGEN (PSCA) ANTIBODIES FOR CANCER TARGETING |
US20080014211A1 (en) * | 2006-07-14 | 2008-01-17 | Mannkind Corporation | Methods to elicit, enhance and sustain immune responses against MHC class I-restricted epitopes, for prophylactic and therapeutic purposes |
AU2008216669B2 (en) * | 2007-02-15 | 2013-12-12 | Mannkind Corporation | A method for enhancing T cell response |
US8877206B2 (en) | 2007-03-22 | 2014-11-04 | Pds Biotechnology Corporation | Stimulation of an immune response by cationic lipids |
JP2010528591A (en) * | 2007-05-23 | 2010-08-26 | マンカインド コーポレイション | Multicistronic vectors and methods for their design |
CA2698343C (en) | 2007-09-04 | 2018-06-12 | The Regents Of The University Of California | High affinity anti-prostate stem cell antigen (psca) antibodies for cancer targeting and detection |
CN110075113A (en) | 2008-04-17 | 2019-08-02 | Pds生物科技公司 | Immune response is stimulated by the enantiomer of cation lipid |
CN104491962B (en) | 2008-06-13 | 2018-10-23 | 曼金德公司 | Diskus and the system conveyed for drug |
US8485180B2 (en) | 2008-06-13 | 2013-07-16 | Mannkind Corporation | Dry powder drug delivery system |
ES2421385T3 (en) | 2008-06-20 | 2013-09-02 | Mannkind Corp | Interactive device and procedure to establish the profile, in real time, of inhalation efforts |
TWI494123B (en) | 2008-08-11 | 2015-08-01 | Mannkind Corp | Use of ultrarapid acting insulin |
AU2009332389A1 (en) | 2008-12-24 | 2011-07-14 | Oncotherapy Science, Inc. | C1orf59 peptides and vaccines including the same |
US8314106B2 (en) | 2008-12-29 | 2012-11-20 | Mannkind Corporation | Substituted diketopiperazine analogs for use as drug delivery agents |
ES2712732T3 (en) | 2009-02-17 | 2019-05-14 | Cornell Res Foundation Inc | Methods and kits for the diagnosis of cancer and the prediction of therapeutic value |
CA2754595C (en) | 2009-03-11 | 2017-06-27 | Mannkind Corporation | Apparatus, system and method for measuring resistance of an inhaler |
US8734845B2 (en) | 2009-06-12 | 2014-05-27 | Mannkind Corporation | Diketopiperazine microparticles with defined specific surface areas |
CA2768149A1 (en) * | 2009-07-14 | 2011-01-20 | Lucia Irene Gonzalez | Stereoisomer peptides and their polymer conjugates for hiv disease |
US8673847B2 (en) * | 2009-10-05 | 2014-03-18 | The Medical College Of Wisconsin, Inc. | Peptide based peroxidase inhibitors and methods of using same |
AU2010310468A1 (en) | 2009-10-23 | 2012-05-24 | Mannkind Corporation | Cancer immunotherapy and method of treatment |
US9016147B2 (en) | 2009-11-03 | 2015-04-28 | Mannkind Corporation | Apparatus and method for simulating inhalation efforts |
EP3511023A1 (en) | 2009-12-02 | 2019-07-17 | Imaginab, Inc. | J591 minibodies and cys-diabodies for targeting human prostate specific membrane antigen (psma) and methods for their use |
EP2582421A1 (en) | 2010-06-21 | 2013-04-24 | MannKind Corporation | Dry powder drug delivery system and methods |
CA2812153C (en) * | 2010-09-20 | 2020-06-30 | Biontech Ag | Antigen-specific t cell receptors and t cell epitopes |
SG10201606220QA (en) | 2011-04-01 | 2016-09-29 | Mannkind Corp | Blister package for pharmaceutical cartridges |
WO2012174472A1 (en) | 2011-06-17 | 2012-12-20 | Mannkind Corporation | High capacity diketopiperazine microparticles |
KR20140095483A (en) | 2011-10-24 | 2014-08-01 | 맨카인드 코포레이션 | Methods and compositions for treating pain |
JP6312262B2 (en) | 2012-07-12 | 2018-04-18 | マンカインド コーポレイション | Dry powder drug delivery system |
CA2885741C (en) | 2012-09-21 | 2023-10-17 | Frank Bedu-Addo | Vaccine comprising r-dotap |
WO2014066856A1 (en) | 2012-10-26 | 2014-05-01 | Mannkind Corporation | Inhalable influenza vaccine compositions and methods |
SG11201507564PA (en) | 2013-03-15 | 2015-10-29 | Mannkind Corp | Microcrystalline diketopiperazine compositions and methods |
JP6769865B2 (en) | 2013-03-15 | 2020-10-14 | ザ トラスティーズ オブ ザ ユニバーシティ オブ ペンシルバニア | Cancer vaccine and treatment method using it |
AU2014290438B2 (en) | 2013-07-18 | 2019-11-07 | Mannkind Corporation | Heat-stable dry powder pharmaceutical compositions and methods |
US11446127B2 (en) | 2013-08-05 | 2022-09-20 | Mannkind Corporation | Insufflation apparatus and methods |
CN104761644A (en) * | 2014-01-03 | 2015-07-08 | 百奇生物科技(苏州)有限公司 | Fusion protein MBP-MART-1 expressed by Escherichia coli, and preparation method and application thereof |
WO2015148905A1 (en) | 2014-03-28 | 2015-10-01 | Mannkind Corporation | Use of ultrarapid acting insulin |
US10816554B2 (en) | 2014-04-04 | 2020-10-27 | The Board Of Trustees Of The Leland Stanford Junior University | Ligand discovery for T cell receptors |
WO2015199617A1 (en) * | 2014-06-24 | 2015-12-30 | National University Of Singapore | A monoclonal antibody with t-cell receptor-like specificity that targets epstein-barr infected human tumour cells based on their expression of ebna1 |
US10561806B2 (en) | 2014-10-02 | 2020-02-18 | Mannkind Corporation | Mouthpiece cover for an inhaler |
EP3331564A4 (en) | 2015-08-07 | 2019-05-22 | Imaginab, Inc. | Antigen binding constructs to target molecules |
CA3005251A1 (en) | 2015-11-13 | 2017-05-18 | Pds Biotechnology Corporation | Lipids as synthetic vectors to enhance antigen processing and presentation ex-vivo in dendritic cell therapy |
EP3468581A1 (en) | 2016-06-13 | 2019-04-17 | Torque Therapeutics, Inc. | Methods and compositions for promoting immune cell function |
GB201616365D0 (en) | 2016-09-27 | 2016-11-09 | Helsingin Yliopisto | Non-genetic modification of enveloped viruses |
WO2018067689A1 (en) | 2016-10-05 | 2018-04-12 | Pds Biotechnology Corporation | Novel hpv16 non hla-restricted t-cell vaccines, compositions and methods of use thereof |
WO2018147960A1 (en) | 2017-02-08 | 2018-08-16 | Imaginab, Inc. | Extension sequences for diabodies |
JP7285828B2 (en) | 2017-09-05 | 2023-06-02 | トルク セラピューティクス, インコーポレイテッド | Therapeutic protein compositions and methods of making and using them |
CN110950949B (en) * | 2018-09-26 | 2022-04-05 | 香雪生命科学技术(广东)有限公司 | T cell receptor for recognizing SSX2 antigen |
CN115819555A (en) * | 2021-09-17 | 2023-03-21 | 香雪生命科学技术(广东)有限公司 | High-affinity TCR for identifying SSX2 |
WO2024092031A1 (en) * | 2022-10-25 | 2024-05-02 | Seismic Therapeutic, Inc. | VARIANT IgG FC POLYPEPTIDES AND USES THEREOF |
Family Cites Families (81)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US613066A (en) * | 1898-10-25 | Bottle-stopper | ||
US4439199A (en) * | 1980-02-19 | 1984-03-27 | Alza Corporation | Method for administering immunopotentiator |
US4683199A (en) * | 1983-01-31 | 1987-07-28 | Sloan-Kettering Institute For Cancer Research | Interleukin-2 dependent cytotoxic T-cell clones |
US5168062A (en) * | 1985-01-30 | 1992-12-01 | University Of Iowa Research Foundation | Transfer vectors and microorganisms containing human cytomegalovirus immediate-early promoter-regulatory DNA sequence |
DE3937412A1 (en) | 1989-11-10 | 1991-05-16 | Hoechst Ag | SYNTHETIC VACCINE FOR THE SPECIFIC INDUCTION OF CYTOTOXIC T-LYMPHOZYTES |
US5093242A (en) * | 1986-10-02 | 1992-03-03 | Massachusetts Institute Of Technology | Methods of generating desired amino-terminal residues in proteins |
US5132213A (en) * | 1986-10-02 | 1992-07-21 | Massachusetts Institute Of Technology | Method for producing proteins and polypeptides using ubiquitin fusions |
US5196321A (en) * | 1986-10-02 | 1993-03-23 | Massachusetts Institute Of Technology | Methods for in vitro cleavage of ubiquitin fusion proteins |
US4937190A (en) * | 1987-10-15 | 1990-06-26 | Wisconsin Alumni Research Foundation | Translation enhancer |
US5258294A (en) * | 1988-02-12 | 1993-11-02 | Commonwealth Scientific And Industrial Research Organisation | Bidirectional pox virus promoter element |
US5804381A (en) | 1996-10-03 | 1998-09-08 | Cornell Research Foundation | Isolated nucleic acid molecule encoding an esophageal cancer associated antigen, the antigen itself, and uses thereof |
US5703055A (en) * | 1989-03-21 | 1997-12-30 | Wisconsin Alumni Research Foundation | Generation of antibodies through lipid mediated DNA delivery |
DK0498851T3 (en) * | 1989-11-03 | 1996-05-13 | Donald L Morton | Tumor-associated urinary antigen, use of antigenic subunits and methods of detection |
SE466259B (en) * | 1990-05-31 | 1992-01-20 | Arne Forsgren | PROTEIN D - AN IGD BINDING PROTEIN FROM HAEMOPHILUS INFLUENZAE, AND THE USE OF THIS FOR ANALYSIS, VACCINES AND PURPOSE |
DE4143467C2 (en) | 1991-05-17 | 1995-02-09 | Max Planck Gesellschaft | Peptide motif and its use |
US5451504A (en) | 1991-07-29 | 1995-09-19 | Serex, Inc. | Method and device for detecting the presence of analyte in a sample |
US6037135A (en) * | 1992-08-07 | 2000-03-14 | Epimmune Inc. | Methods for making HLA binding peptides and their uses |
DE4228458A1 (en) * | 1992-08-27 | 1994-06-01 | Beiersdorf Ag | Multicistronic expression units and their use |
US5405940A (en) * | 1992-08-31 | 1995-04-11 | Ludwig Institute For Cancer Research | Isolated nonapeptides derived from MAGE genes and uses thereof |
DE4238416A1 (en) | 1992-11-13 | 1994-05-19 | Max Planck Gesellschaft | Determination of peptide motifs on MHC molecules |
US5744316A (en) * | 1992-12-22 | 1998-04-28 | Ludwig Institute For Cancer Research | Isolated, tyrosinase derived peptides and uses thereof |
US5519117A (en) * | 1992-12-22 | 1996-05-21 | Ludwig Institute For Cancer Research | Isolated, tyrosinase derived peptides and uses thereof |
US5487974A (en) * | 1992-12-22 | 1996-01-30 | Ludwig Institute For Cancer-Research | Method for detecting complexes containing human leukocyte antigen A2 (HLA-A2) molecules and a tyrosinase drived peptide on abnormal cells |
US5530096A (en) * | 1992-12-22 | 1996-06-25 | Ludwig Institute For Cancer Research | Isolated, tyrosinase derived peptides and uses thereof |
US5558995A (en) * | 1993-01-22 | 1996-09-24 | Ludwig Institute For Cancer Research | Peptides which are derived from tumor rejection antigen precursor molecule MAGE-1, which complex to MHC molecule HLA-C clone 10, and uses thereof |
US5989565A (en) * | 1993-01-29 | 1999-11-23 | University Of Pittsburgh | Elution and identification of T cell epitopes from viable cells |
WO1994021680A1 (en) * | 1993-03-17 | 1994-09-29 | The Government Of The United States Of America As | Immunogenic chimeras comprising nucleic acid sequences encoding endoplasmic reticulum signal sequence peptides and at least one other peptide, and their uses in vaccines and disease treatments |
US5648226A (en) * | 1993-07-22 | 1997-07-15 | Ludwig Institute For Cancer Research | Isolated peptides derived from tumor rejection antigens, and their use |
US5679647A (en) * | 1993-08-26 | 1997-10-21 | The Regents Of The University Of California | Methods and devices for immunizing a host against tumor-associated antigens through administration of naked polynucleotides which encode tumor-associated antigenic peptides |
US5478556A (en) * | 1994-02-28 | 1995-12-26 | Elliott; Robert L. | Vaccination of cancer patients using tumor-associated antigens mixed with interleukin-2 and granulocyte-macrophage colony stimulating factor |
US5585461A (en) * | 1994-03-24 | 1996-12-17 | Ludwig Institute For Cancer Research | Isolated, MAGE-3 derived peptides which complex with HLA-A2 molecules and uses thereof |
US5554506A (en) * | 1994-03-24 | 1996-09-10 | Ludwig Institute For Cancer Research | Isolated, MAGE-3 derived peptides which complex with HLA-A2 molecules and uses thereof |
US5554724A (en) * | 1994-03-24 | 1996-09-10 | University Of Leiden | Isolated tumor rejection antigen precursor MAGE-2 derived peptides, and uses thereof |
US5874560A (en) * | 1994-04-22 | 1999-02-23 | The United States Of America As Represented By The Department Of Health And Human Services | Melanoma antigens and their use in diagnostic and therapeutic methods |
IT1266740B1 (en) * | 1994-07-01 | 1997-01-14 | Maria Paola Landini | RECOMBINANT PROTEIN MATERIAL BINDING ANTIBODIES AGAINST HUMAN CYTOMEGALOVIRUS, DIAGNOSTIC REAGENTS DERIVED FROM THIS |
DE4423392A1 (en) | 1994-07-04 | 1996-01-11 | Birsner & Grob Biotech Gmbh | Methods of identifying antigenic peptides |
FR2722208B1 (en) * | 1994-07-05 | 1996-10-04 | Inst Nat Sante Rech Med | NEW INTERNAL RIBOSOME ENTRY SITE, VECTOR CONTAINING SAME AND THERAPEUTIC USE |
EP0769963A4 (en) | 1994-07-27 | 1999-07-28 | Commw Scient Ind Res Org | Polyepitope vaccines |
US5962428A (en) * | 1995-03-30 | 1999-10-05 | Apollon, Inc. | Compositions and methods for delivery of genetic material |
US5698396A (en) * | 1995-06-07 | 1997-12-16 | Ludwig Institute For Cancer Research | Method for identifying auto-immunoreactive substances from a subject |
CA2249390C (en) | 1996-03-19 | 2007-12-18 | University Of Virginia Patent Foundation | Peptides recognized by melanoma-specific a1-, a2- and a3-restricted cytotoxic lymphocytes, and uses therefor |
JP4108126B2 (en) | 1996-04-26 | 2008-06-25 | リュクスウニヴェルシテート テ レイデン | T cell peptide epitope selection and production method and vaccine incorporating the selected epitope |
US5876972A (en) | 1996-09-23 | 1999-03-02 | Max-Planck-Gesellschaft Zur Forderung Der Wissenschaften E.V. | Nucleic acid molecules coding for tumor suppressor proteins and methods for their isolation |
US5990091A (en) | 1997-03-12 | 1999-11-23 | Virogenetics Corporation | Vectors having enhanced expression, and methods of making and uses thereof |
US6004777A (en) * | 1997-03-12 | 1999-12-21 | Virogenetics Corporation | Vectors having enhanced expression, and methods of making and uses thereof |
US6287569B1 (en) * | 1997-04-10 | 2001-09-11 | The Regents Of The University Of California | Vaccines with enhanced intracellular processing |
EP1003548B1 (en) | 1997-07-10 | 2006-05-10 | Mannkind Corporation | Device for inducing a ctl response |
US7084239B1 (en) * | 1997-10-08 | 2006-08-01 | The United States Of America As Represented By The Department Of Health And Human Services | Cancer peptides of NY-ESO-1/CAG-3 |
CA2309344A1 (en) * | 1997-11-12 | 1999-05-20 | Valentis, Inc. | Expression plasmids for multiepitope nucleic acid-based vaccines |
US20030138808A1 (en) | 1998-02-19 | 2003-07-24 | Simard John J.L. | Expression vectors encoding epitopes of target-associated antigens |
CA2323632A1 (en) | 1998-03-13 | 1999-09-16 | Epimmune Inc. | Hla-binding peptides and their uses |
US6495136B1 (en) * | 1998-03-26 | 2002-12-17 | The Procter & Gamble Company | Proteases having modified amino acid sequences conjugated to addition moieties |
GB9808932D0 (en) | 1998-04-27 | 1998-06-24 | Chiron Spa | Polyepitope carrier protein |
IL125608A0 (en) | 1998-07-30 | 1999-03-12 | Yeda Res & Dev | Tumor associated antigen peptides and use of same as anti-tumor vaccines |
US6800730B1 (en) * | 1998-10-02 | 2004-10-05 | Ludwig Institute For Cancer Research | Isolated peptides which bind to MHC class II molecules, and uses thereof |
WO2000029008A2 (en) | 1998-11-16 | 2000-05-25 | Board Of Regents, The University Of Texas System | Hiv-specific t-cell induction |
AU2720600A (en) | 1999-01-08 | 2000-07-24 | Powderject Vaccines, Inc. | Vaccination method for efficient induction of cytotoxic t lymphocyte response |
EP1157267B1 (en) | 1999-03-03 | 2016-10-05 | Olympus Corporation | Fluorescence binding assay method |
DE19909503A1 (en) | 1999-03-04 | 2000-09-07 | Boehringer Ingelheim Int | Tumor Associated Antigen |
DE19919225A1 (en) | 1999-04-28 | 2000-11-16 | Boehringer Ingelheim Int | Tumor Associated Antigen |
AU5299800A (en) | 1999-05-26 | 2000-12-12 | Oregon Health And Science University | Tagged epitope protein transposable element |
DE19924199A1 (en) | 1999-05-27 | 2000-11-30 | Boehringer Ingelheim Int | Tumor Associated Antigen |
FR2794370B1 (en) | 1999-06-03 | 2003-10-17 | Biovector Therapeutics | POLYEPITOPIC PROTEIN FRAGMENTS, THEIR OBTAINMENT AND THEIR USES IN PARTICULAR IN VACCINATION |
DE19936563A1 (en) | 1999-08-04 | 2001-02-08 | Boehringer Ingelheim Int | Tumor Associated Antigen |
CA2383737C (en) | 1999-09-08 | 2011-01-18 | Transgene S.A. | Muc-1 derived peptides |
EP1214097B3 (en) | 1999-09-16 | 2011-07-20 | Eisai Inc. | Nucleic acids encoding polyepitope polypeptides |
WO2001023577A2 (en) | 1999-09-30 | 2001-04-05 | Institut Pasteur | Hybrid or chimeric polynucleotides, proteins, and compositions comprising hepatitis b virus sequences |
EP1118860A1 (en) * | 2000-01-21 | 2001-07-25 | Rijksuniversiteit te Leiden | Methods for selecting and producing T cell peptide epitopes and vaccines incorporating said selected epitopes |
AU785151B2 (en) * | 2000-01-28 | 2006-10-05 | Government Of The United States Of America, As Represented By The Secretary Of The Department Of Health And Human Services, The | Novel MHC class II restricted T cell epitopes from the cancer antigen, NY ESO-1 |
US6756044B1 (en) | 2000-02-09 | 2004-06-29 | Genvec, Inc. | Antigenic complexes and methods |
WO2001062917A1 (en) * | 2000-02-22 | 2001-08-30 | Ludwig Institute For Cancer Research | Isolated genomic sequences which encode the ny-eso-1 cancer testis tumor antigen and uses thereof |
EP2278023A1 (en) | 2000-04-28 | 2011-01-26 | Mannkind Corporation | Epitope cluster from Melan-A/MART-1 for the induction of anti-tumor immunogenicity |
US20030215425A1 (en) * | 2001-12-07 | 2003-11-20 | Simard John J. L. | Epitope synchronization in antigen presenting cells |
DE10025521A1 (en) | 2000-05-23 | 2001-12-06 | Boehringer Ingelheim Int | Tumor-associated antigen B132 |
AUPQ776100A0 (en) | 2000-05-26 | 2000-06-15 | Australian National University, The | Synthetic molecules and uses therefor |
CU23235A1 (en) | 2001-02-28 | 2007-09-26 | Ct Ingenieria Genetica Biotech | RECOMBINANT POXVIRUS FOR CHEMICAL PROTEINS OF THE HUMAN IMMUNODEFICIENCY VIRUS AND ITS APPLICATION IN THERAPEUTICS AND AIDS PREVENTION |
WO2003008537A2 (en) * | 2001-04-06 | 2003-01-30 | Mannkind Corporation | Epitope sequences |
GB0118532D0 (en) * | 2001-07-30 | 2001-09-19 | Isis Innovation | Materials and methods relating to improved vaccination strategies |
EP2314712B1 (en) * | 2001-11-07 | 2014-01-08 | Mannkind Corporation | Expression vectors encoding epitopes of antigens and methods for their design |
JP4179585B2 (en) | 2002-03-29 | 2008-11-12 | ユニ・チャーム株式会社 | Printed biodegradable plastic film |
WO2004022709A2 (en) | 2002-09-06 | 2004-03-18 | Mannkind Corporation | Epitope sequences |
-
2002
- 2002-11-07 EP EP20100180603 patent/EP2314712B1/en not_active Expired - Lifetime
- 2002-11-07 WO PCT/US2002/036098 patent/WO2003063770A2/en not_active Application Discontinuation
- 2002-11-07 DE DE60238864T patent/DE60238864D1/en not_active Expired - Lifetime
- 2002-11-07 DK DK02806695T patent/DK1453471T3/en active
- 2002-11-07 ES ES02806695T patent/ES2358642T3/en not_active Expired - Lifetime
- 2002-11-07 US US10/292,413 patent/US8637305B2/en not_active Expired - Fee Related
- 2002-11-07 CA CA 2469738 patent/CA2469738A1/en not_active Abandoned
- 2002-11-07 CN CNB028268563A patent/CN1313617C/en not_active Expired - Fee Related
- 2002-11-07 EP EP20020806695 patent/EP1453471B1/en not_active Expired - Lifetime
- 2002-11-07 MX MXPA04005382A patent/MXPA04005382A/en active IP Right Grant
- 2002-11-07 AT AT02806695T patent/ATE494387T1/en not_active IP Right Cessation
- 2002-11-07 CN CNA2007100881606A patent/CN101024842A/en active Pending
-
2004
- 2004-02-10 US US10/777,053 patent/US7232682B2/en not_active Expired - Fee Related
- 2004-04-30 US US10/837,217 patent/US8252916B2/en not_active Expired - Fee Related
-
2005
- 2005-02-22 HK HK05101449A patent/HK1068807A1/en not_active IP Right Cessation
- 2005-10-31 HK HK05109682A patent/HK1075473A1/en not_active IP Right Cessation
-
2008
- 2008-09-30 AU AU2008229722A patent/AU2008229722B2/en not_active Ceased
Also Published As
Publication number | Publication date |
---|---|
WO2003063770A2 (en) | 2003-08-07 |
DE60238864D1 (en) | 2011-02-17 |
US20030228634A1 (en) | 2003-12-11 |
CN1313617C (en) | 2007-05-02 |
AU2008229722A1 (en) | 2008-10-30 |
US20040203051A1 (en) | 2004-10-14 |
US7232682B2 (en) | 2007-06-19 |
US8252916B2 (en) | 2012-08-28 |
EP2314712A1 (en) | 2011-04-27 |
EP1453471A2 (en) | 2004-09-08 |
EP2314712B1 (en) | 2014-01-08 |
DK1453471T3 (en) | 2011-03-28 |
HK1075473A1 (en) | 2005-12-16 |
ATE494387T1 (en) | 2011-01-15 |
MXPA04005382A (en) | 2005-02-24 |
ES2358642T3 (en) | 2011-05-12 |
WO2003063770A3 (en) | 2004-04-01 |
HK1068807A1 (en) | 2005-05-06 |
AU2008229722B2 (en) | 2012-09-06 |
WO2003063770A9 (en) | 2004-06-17 |
EP1453471B1 (en) | 2011-01-05 |
US20040132088A1 (en) | 2004-07-08 |
US8637305B2 (en) | 2014-01-28 |
CN101024842A (en) | 2007-08-29 |
EP1453471A4 (en) | 2006-11-29 |
CN1612935A (en) | 2005-05-04 |
Similar Documents
Publication | Publication Date | Title |
---|---|---|
US8252916B2 (en) | Expression vectors encoding epitopes of target-associated antigens and methods for their design | |
US9795666B2 (en) | High-yield transgenic mammalian expression system for generating virus-like particles | |
Wu et al. | Mammalian expression of virus-like particles for advanced mimicry of authentic influenza virus | |
EP1787654B1 (en) | Intralymphatic immunization for inducing sustained effector CTL responses | |
AU2021201844A1 (en) | High titer recombinant influenza viruses with enhanced replication in mdck or vero cells or eggs | |
US20070184062A1 (en) | Epitope synchronization in antigen presenting cells | |
Hessel et al. | Vectors based on modified vaccinia Ankara expressing influenza H5N1 hemagglutinin induce substantial cross-clade protective immunity | |
CA2529056C (en) | Combinations of tumor-associated antigens in compositions for various types of cancers | |
CA3119752A1 (en) | Alphavirus neoantigen vectors and interferon inhibitors | |
US20230024133A1 (en) | Prostate Neoantigens And Their Uses | |
Zhou et al. | Hexon-modified recombinant E1-deleted adenovirus vectors as dual specificity vaccine carriers for influenza virus | |
Rosendahl Huber et al. | Chemical modification of influenza CD8+ T-cell epitopes enhances their immunogenicity regardless of immunodominance | |
Vertuani et al. | HER-2/neu mediated down-regulation of MHC class I antigen processing prevents CTL-mediated tumor recognition upon DNA vaccination in HLA-A2 transgenic mice | |
CA2494304A1 (en) | Materials and methods relating to improved vaccination strategies | |
US20230029453A1 (en) | Prostate Neoantigens And Their Uses | |
Wang et al. | Alphavirus replicon particles containing the gene for HER2/neu inhibit breast cancer growth and tumorigenesis | |
AU2008229888B2 (en) | Expression vectors encoding epitopes of target-associated antigens and methods for their design | |
Toshitani et al. | Expression of a single-chain HLA class I molecule in a human cell line: presentation of exogenous peptide and processed antigen to cytotoxic T lymphocytes. | |
CA2331378A1 (en) | Vaccination strategy to prevent and treat cancers | |
Durantez et al. | Induction of Multiepitopic and Long‐Lasting Immune Responses Against Tumour Antigens by Immunization with Peptides, DNA and Recombinant Adenoviruses Expressing Minigenes | |
Cheung et al. | Two novel HLA-A* 0201 T-cell epitopes in avian H5N1 viral nucleoprotein induced specific immune responses in HHD mice | |
AU2002365932A1 (en) | Expression vectors encoding epitopes of target-associated antigens and methods for their design | |
Song et al. | Evaluation of antitumor immunity efficacy of epitope-based vaccine with B16 cell line coexpressing HLA-A2/H-2kb and CTL multiepitope in HLA transgenic mice | |
Hospers et al. | Construction of a triple modified p53 containing DNA vaccine to enhance processing and presentation of the p53 antigen |
Legal Events
Date | Code | Title | Description |
---|---|---|---|
EEER | Examination request | ||
FZDE | Discontinued |
Effective date: 20150526 |